[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"      "-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/11541686/OV-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/11551026/transformed.cor.cli.txt"

nPatients in clinical file=588, in cluster file=579, common to both=571
[1]  71 571
[1] "AMP PEAK  1(1P34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          289                           282 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          289                           282 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          363                           208 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          363                           208 
[1] "AMP PEAK  3(1Q42.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          315                           256 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          315                           256 
[1] "AMP PEAK  4(2P23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          246                           325 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          246                           325 
[1] "AMP PEAK  5(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          259                           312 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          259                           312 
[1] "AMP PEAK  6(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          477                            94 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          477                            94 
[1] "AMP PEAK  7(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                          158                           413 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                          158                           413 
[1] "AMP PEAK  8(4Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                          113                           458 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                          113                           458 
[1] "AMP PEAK  9(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           305                            266 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           305                            266 
[1] "AMP PEAK 10(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          298                           273 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          298                           273 
[1] "AMP PEAK 11(7Q36.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          314                           257 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          314                           257 
[1] "AMP PEAK 12(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           209                            362 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           209                            362 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           453                            118 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           453                            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                            321 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           250                            321 
[1] "AMP PEAK 15(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                           181                            390 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                           181                            390 
[1] "AMP PEAK 16(11Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           253                            318 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           253                            318 
[1] "AMP PEAK 17(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            327                             244 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            327                             244 
[1] "AMP PEAK 18(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           311                            260 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           311                            260 
[1] "AMP PEAK 19(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         220                          351 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         220                          351 
[1] "AMP PEAK 20(14Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                           146                            425 
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                           146                            425 
[1] "AMP PEAK 21(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                            155                             416 
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                            155                             416 
[1] "AMP PEAK 22(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           159                            412 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           159                            412 
[1] "AMP PEAK 23(17Q25.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           212                            359 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           212                            359 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           139                            432 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           139                            432 
[1] "AMP PEAK 25(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            312                             259 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            312                             259 
[1] "AMP PEAK 26(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         317                          254 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         317                          254 
[1] "AMP PEAK 27(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           241                            330 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           241                            330 
[1] "AMP PEAK 28(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         314                          257 
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         314                          257 
[1] "AMP PEAK 29(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            342                             229 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            342                             229 
[1] "AMP PEAK 30(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            397                             174 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            397                             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                            480 
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            91                            480 
[1] "AMP PEAK 32(XP11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                           158                            413 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                           158                            413 
[1] "AMP PEAK 33(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        216                         355 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        216                         355 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           265                            306 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           265                            306 
[1] "DEL PEAK  2(1Q41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         94                         477 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         94                         477 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          120                           451 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          120                           451 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          134                           437 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          134                           437 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          172                           399 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          172                           399 
[1] "DEL PEAK  6(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          206                           365 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          206                           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                            487 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            84                            487 
[1] "DEL PEAK  8(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          389                           182 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          389                           182 
[1] "DEL PEAK  9(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          415                           156 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          415                           156 
[1] "DEL PEAK 10(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          349                           222 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          349                           222 
[1] "DEL PEAK 11(5Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          413                           158 
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          413                           158 
[1] "DEL PEAK 12(6Q27) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        373                         198 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        373                         198 
[1] "DEL PEAK 13(7P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                          250                           321 
  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                          250                           321 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          383                           188 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          383                           188 
[1] "DEL PEAK 15(8P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          400                           171 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          400                           171 
[1] "DEL PEAK 16(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          259                           312 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          259                           312 
[1] "DEL PEAK 17(9Q34.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           340                            231 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           340                            231 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           117                            454 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           117                            454 
[1] "DEL PEAK 19(10Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                           250                            321 
  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                           250                            321 
[1] "DEL PEAK 20(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           340                            231 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           340                            231 
[1] "DEL PEAK 21(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         200                          371 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         200                          371 
[1] "DEL PEAK 22(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                            214                             357 
  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                            214                             357 
[1] "DEL PEAK 23(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           358                            213 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           358                            213 
[1] "DEL PEAK 24(14Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           301                            270 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           301                            270 
[1] "DEL PEAK 25(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                           295                            276 
  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                           295                            276 
[1] "DEL PEAK 26(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                           359                            212 
  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                           359                            212 
[1] "DEL PEAK 27(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                           308                            263 
  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                           308                            263 
[1] "DEL PEAK 28(16Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                           456                            115 
  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                           456                            115 
[1] "DEL PEAK 29(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           446                            125 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           446                            125 
[1] "DEL PEAK 30(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         485                           86 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         485                           86 
[1] "DEL PEAK 31(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                           466                            105 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                           466                            105 
[1] "DEL PEAK 32(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         376                          195 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         376                          195 
[1] "DEL PEAK 33(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           504                             67 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           504                             67 
[1] "DEL PEAK 34(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                            294                             277 
  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                            294                             277 
[1] "DEL PEAK 35(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            280                             291 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            280                             291 
[1] "DEL PEAK 36(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                           223                            348 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                           223                            348 
[1] "DEL PEAK 37(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                            496                              75 
  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                            496                              75 
[1] "DEL PEAK 38(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                          352                           219 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                          352                           219 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                                      
 [2] "VITALSTATUS"                                       
 [3] "DAYSTODEATH"                                       
 [4] "DAYSTOLASTFOLLOWUP"                                
 [5] "PRIMARYSITEOFDISEASE"                              
 [6] "NEOPLASM.DISEASESTAGE"                             
 [7] "PATHOLOGY.T.STAGE"                                 
 [8] "PATHOLOGY.N.STAGE"                                 
 [9] "PATHOLOGY.M.STAGE"                                 
[10] "DCCUPLOADDATE"                                     
[11] "GENDER"                                            
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"                  
[13] "RADIATIONTHERAPY"                                  
[14] "KARNOFSKYPERFORMANCESCORE"                         
[15] "EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE"
[16] "HISTOLOGICALTYPE"                                  
[17] "TUMORGRADE"                                        
[18] "TUMORSTAGE"                                        
[19] "PATIENTTUMORRECURRENCESTATUS"                      
[20] "DAYSTOTUMORRECURRENCE"                             
[21] "CHEMOTHERAPY"                                      
[22] "RADIATIONS.RADIATION.REGIMENINDICATION"            
[23] "COMPLETENESS.OF.RESECTION"                         
[24] "RACE"                                              
[25] "ETHNICITY"                                         
[26] "BATCHNUMBER"                                       

Input Data has 26 rows and 571 columns.

[1] "Batch" "26"   
[1] "Last Follow UP"
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
        1224         1247           55         1495           NA         1418 
TCGA-04-1341 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
          NA           NA           NA         1993         1919           NA 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1357 TCGA-04-1360 
          NA           NA         1991           NA           NA           NA 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
         989           NA           NA         2329         2174         2506 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1519 TCGA-04-1525 TCGA-04-1530 
          NA         1265           NA           NA         1167           NA 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
          NA           NA           NA           NA           NA           NA 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
        1966           NA           NA           NA           NA           NA 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
          NA           NA           NA           NA           NA           NA 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
          NA           NA           NA         1752         1882         1684 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
         928          547          178           92          260         2967 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
         188          186           NA           NA         3419         2163 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
        1919         1209          637          819          379         1652 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
         788         2478          563         1011          982          356 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
         119         1078         1089          460          604          189 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
         748         1355         1204           83          377          946 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
         462          542         1678           76          340          346 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
         351         1036          981          944          651          257 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
        1184         1117          873          923          596          265 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
         237          247          252          249         1334         1073 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
        1073          414         2097         3260         2780         2259 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
        2028         2141         1881         2068         2099         1319 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
        1748         1708         1736          589         1441         1470 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
        1455         1367         1364         1128          843         1036 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
         912          644          453          420          141          195 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
         185          331          201          224          184          180 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
         208          143          128          162         1662         2648 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
        1877          895         2982          629          681         2154 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
        2521         1595         2237         1162         1498          129 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
        1652         1144         1168          425          999          504 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
         128          134          145          127           78          119 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
          94          433          372          262          328          266 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
         191         1666           NA           NA          789          797 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
        2196          837          772          581          508           89 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
          81         1446         1294         1233          468          816 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
         966         1503          268          886          575           68 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        1562         1658           98          949         2089          139 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
        1013         2616         3953          130          194         1189 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
        1018         1768           16          759         3525         2661 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 
        2788         2342         1516           84          143          137 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
         232          598          354          663         1264          233 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
         679         1646         1933         1442          192          194 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
         238          243          239           23          190          183 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
         181          163          147          529          863          583 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
         568         1324          260         2218          379         1373 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        3224          277          105           36          676          820 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
        1746         1955          493         1721         1249         1579 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
        1259         1767         2692         2148         1213          594 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
        1341         1384         1451          787          312          524 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 
        2742         2688         1470         1163          253          106 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
         113          116          133          343          176          168 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
         298          690          919          500          336         2467 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 
         148         4624         1364         1769         1059         3337 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
         439         1641          562          857         1947         1354 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
        1736         1100           24           11         1446          962 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
        2143         1357           25         2049         1102          506 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
        1007         1699         1620           31          820          974 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
        1553         1126           31         1064         1977         1124 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
        1033           91          365           90          565          548 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
         481           11          627          239            9         1732 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
        1843         1081         1558          455          760          549 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
        2587          396         1492           31         1157           92 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 
         365         1369          608         1278           90          883 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 
         943          821         2400         1360         1435         3096 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
        1172           24         1025          949         2078           16 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
         514          568         1815          555         1277          889 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
        1053          517         2606         2032         1914         1190 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
         950          699          741          686          527          376 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
         360          374          454          255          220          163 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        1053         2621         1977         1900         1372          149 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
        1285          360          349          297          640         1158 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        1579         1103           75          477            8         1463 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 
        1366         1058          186         1114           37         1751 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
         738          914         1484         1386          918          571 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
         684          204         1293         1342           67          875 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 
         885          655          695          686          260          915 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
         783          847          737          751         1066         1004 
TCGA-36-2532 TCGA-36-2533 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
         897           NA          907          788          763          724 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
         657           68          638          557          624          431 
TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
         184          492          349          243          792          722 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
         287         1278          227         1240           NA          731 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
         346          643           53          679          882          763 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
         761         5481           NA           NA         3532           NA 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
          NA           NA          165           NA           NA          338 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
         246          637          956          564          848          132 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
         967          866         1484         1364         1089           74 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        1024         1329           44          256          176          347 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
         396          276         1038          952         1127         1293 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 
        1488         1722         2061         1321          479         1161 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
          61          168          441          547          122          932 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
        1212          932           36         1398         1381          146 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 
         145         1573         2182         1875         1776         1844 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
        1993         1688          197         2338          629         1354 
TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-72-4231 
        3825          676          193          945          262           NA 
TCGA-72-4232 TCGA-72-4233 TCGA-72-4234 TCGA-72-4235 TCGA-72-4236 TCGA-72-4237 
          NA           NA           NA           NA           NA           NA 
TCGA-72-4238 TCGA-72-4240 TCGA-72-4241 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
          NA           NA           NA         1207          576           NA 
TCGA-WR-A838 
         245 
Variable 1:'AGE':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=267,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=452,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'EXAMINATIONS.EXAMINATION.KARNOFSKYPERFORMANCESCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'TUMOR.GRADE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TUMOR.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'PATIENTTUMORRECURRENCESTATUS':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'DAYSTOTUMORRECURRENCE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'CHEMOTHERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 24:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 25:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 26:'BATCH.NUMBER':	nDistinctValues=21,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "PRIMARY.SITE.OF.DISEASE"               
[3] "KARNOFSKY.PERFORMANCE.SCORE"           
[4] "RADIATIONS.RADIATION.REGIMENINDICATION"
[5] "COMPLETENESS.OF.RESECTION"             
[6] "RACE"                                  
[7] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 571 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=55, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, 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   149 133
  AMP PEAK  1(1P34.3) WILD-TYPE 117 157
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          282                           274 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          133                           157 
$`AMP PEAK  1(1P34.3) MUTATED`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       41.00        49.15        18.51        11.87        65.52        63.09 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       65.46        49.28        32.52        76.57        71.47        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       41.59        19.99        38.37       119.08        29.10        55.43 
TCGA-04-1649 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1667 
       64.64        29.16         9.47        57.76        17.98        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-10-0928 
       71.11        63.09        39.75        26.93        12.46        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0751 
       33.24        32.28        39.58         2.73        31.10        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0797 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 
       38.93        30.35         8.71         8.19        43.86        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 
       68.94       107.18        74.27        70.39        67.99        43.36 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 TCGA-13-0916 
       48.33        47.84        44.94        44.84        27.72        21.17 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         4.64         6.41        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1491 
        6.05         4.70         5.33        87.06        61.71        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1504 
       73.55        49.25         4.24        54.31        37.61        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 
        4.21         4.41         4.77         4.18         2.56        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU 
       12.23         8.61        10.78         8.75        54.77         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-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       40.54        15.39        26.83        49.41         8.81        18.90 
TCGA-23-1109 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
       51.35        68.68        86.01       129.96         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 
       33.47        58.13         0.53        24.95       115.89        91.66 
TCGA-23-2084 TCGA-23-2643 TCGA-24-0966 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
       49.84         4.70         7.63        41.56        22.32        63.55 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
        7.82         7.99         0.76         6.02         4.83        17.39 
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-24-1549 TCGA-24-1551 
        9.11         3.45         1.18        22.22        56.58        51.91 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1567 
       58.09        39.88        19.53        44.09        25.87        17.23 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1920 TCGA-24-1924 
       48.33        38.24         8.32         3.81         9.80        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 
       11.05        81.11       152.02        34.82        53.95        18.48 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       57.07        36.16         0.36        31.63        70.45        44.61 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.82        36.23        33.11        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
       26.96        51.06        65.00         2.96        18.58        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-2391 
        0.36        20.61        60.59        35.54        51.22        49.05 
TCGA-25-2392 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-29-1691 TCGA-29-1693 
        1.02        12.00        45.01        42.02        47.18       101.79 
TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       68.32        16.90        18.67        41.98        29.23        17.00 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       62.93        39.12        24.36        22.55        17.33        12.36 
TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2431 
       12.30        14.93         7.23         5.36        65.00        42.25 
TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       11.84        21.04        38.07        51.91         2.47        15.68 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
       44.91        34.78         6.12        36.62         1.22        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 
       30.05        48.79        45.57        18.77        42.51         2.20 
TCGA-36-1568 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2544 
       28.77        25.74        27.85        24.23        24.69        20.98 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 
       20.52        14.17         6.05        16.18        26.04         9.44 
TCGA-42-2589 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 
       42.02        11.38        21.14         1.74        22.32        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-61-1724 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-61-1899 
       28.47        44.84        35.80         2.43        33.67         8.42 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       34.13        31.30        48.92        56.61        67.76        15.75 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2012 TCGA-61-2088 
       38.17         5.52        14.50         4.01        30.64         4.77 
TCGA-61-2097 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-OY-A56P 
       60.62         6.48        76.87        20.68       125.75        39.68 

$`AMP PEAK  1(1P34.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1348 TCGA-04-1349 
       40.24         1.81         2.01        46.62        48.76        21.57 
TCGA-04-1350 TCGA-04-1362 TCGA-04-1364 TCGA-04-1514 TCGA-04-1542 TCGA-04-1644 
       63.98        44.32        33.67        56.55        84.20        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       27.88        28.64        36.23        31.86        47.70        45.37 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 TCGA-09-1674 TCGA-09-2044 
       57.60        55.36        30.51         5.85         8.55         6.12 
TCGA-09-2045 TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 
       35.15        20.94        54.31        25.91        81.47        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        3.91        35.44        35.80        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 
       24.59        44.55        12.39        15.19        17.82         2.50 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0799 
       11.54        34.06        36.72        28.70        19.59         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0885 TCGA-13-0887 
        8.12         8.28        35.28        35.28        91.40        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       61.84        69.01        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0924 
       47.38        37.08        34.06        29.98        14.89         6.08 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1477 TCGA-13-1483 TCGA-13-1484 
        5.92         6.84         4.21        54.64        29.42        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1494 TCGA-13-1499 
       20.68        22.39        70.82        82.88        38.20        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1511 TCGA-13-1512 TCGA-13-2071 TCGA-20-0996 
       13.97        32.84         3.91         3.09         6.28        72.20 
TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1027 
       25.38         2.93         2.66        47.54        42.54        31.76 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       29.13         2.24        54.51         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1121 TCGA-23-2078 TCGA-23-2081 TCGA-23-2641 TCGA-23-2645 
       33.30         6.38        87.48        77.00         2.76         4.50 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 
       19.66        11.64        21.80         7.66        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.31         6.38         7.86         6.25         5.95         5.36 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1467 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       28.37        19.17       105.99        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1562 
       16.21        41.06        41.39        88.50        70.62        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 TCGA-24-1844 
       47.70        10.26        90.15        88.37         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1927 
        4.37        11.28         5.79         5.52        22.68        16.44 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 
        4.87        44.84        58.16       109.71        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2261 TCGA-24-2267 TCGA-24-2289 TCGA-24-2293 
       64.01        44.52         0.79        47.54        67.36        16.64 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       32.02        37.02         1.02        34.98        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
        2.99        12.00        18.02         7.86         0.30        56.94 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2393 
       14.96        24.99        18.05        85.05        13.02        38.04 
TCGA-25-2396 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
        3.02        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 
       78.90        44.71        38.53         0.79        33.70        31.20 
TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 
        0.53        59.67        18.25        34.62        85.68        66.81 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 
       31.23        22.98        11.84         8.38        34.62        86.17 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 TCGA-30-1853 
       62.47        45.11         4.90        11.47         9.76        36.26 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1880 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
        0.26        48.10        57.57        30.18        22.49         6.71 
TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       44.12        29.10        21.53        22.85        22.55         8.55 
TCGA-36-1576 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       30.08        35.05        33.01        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2552 
       25.08        23.80        21.60         2.24        18.31        11.47 
TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        7.99        23.74         7.46        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-59-A5PD TCGA-61-1721 TCGA-61-1736 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 
       20.52        11.11        48.79        43.69         1.45         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 
       11.41        13.02         9.07        37.05        42.51        43.43 
TCGA-61-1995 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
        2.01        17.98        30.64        39.85         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-61-2098 TCGA-61-2101 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       65.52        55.50        44.52        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        18.94         0.79         8.05 

  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                        109.71 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                        27.62                         28.67 
[1] "0.4 - 180.2 (27.6)" "0.3 - 109.7 (28.7)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  1(1P34.3) MUTATED         1   282                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                                    1                             1
  OVARY                                    282                           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, continuous
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     3 286
  AMP PEAK  1(1P34.3) WILD-TYPE   0 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      3  286
  AMP PEAK  1(1P34.3) WILD-TYPE    0  282
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  NO                            3                             0
  YES                         286                           282
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  1(1P34.3) MUTATED    7  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                           7                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P34.3) MUTATED                                  0     6
  AMP PEAK  1(1P34.3) WILD-TYPE                                3    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P34.3) MUTATED                          13
  AMP PEAK  1(1P34.3) WILD-TYPE                        19
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P34.3) MUTATED                                           1   251
  AMP PEAK  1(1P34.3) WILD-TYPE                                         0   224
D1V7, multiclass
                                           clus
vv                                          AMP PEAK  1(1P34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             251
                                           clus
vv                                          AMP PEAK  1(1P34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               224
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED     5 165
  AMP PEAK  1(1P34.3) WILD-TYPE   5 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      5  165
  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                         165
                        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   160 191
  AMP PEAK  2(1Q21.3) WILD-TYPE 106  99
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          351                           205 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          191                            99 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24        41.00        46.62        18.51        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 
       63.09        48.76        65.46        49.28        44.32        33.67 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        41.59        19.99        38.37       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       84.20        55.43        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       45.37        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 
        9.99        38.43        41.62        61.87        55.36        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 
        5.85         3.02         8.55         6.18        35.15       112.41 
TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0930 
       63.09        20.94        26.93        12.46        54.31        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       32.28        11.70         3.91        35.44        35.80        19.86 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       24.59        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 
       55.17        11.18        11.54        34.06        32.25         8.45 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       38.93        30.35        19.59         8.71         7.79         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 
        8.19        43.86        13.61        68.94        91.40        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 
       19.36        48.33        47.84        37.08        27.72        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       13.81         4.64         6.41         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
        4.70         4.21        54.64        87.06        61.71        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 
       20.68        22.39        70.82        82.88        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       54.31        37.61        38.40        16.57         4.21         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.61        10.78         8.75         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        42.54 
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-24-0968 TCGA-24-0979 TCGA-24-0982 
       49.84         4.70         4.50        19.66        41.56        22.32 
TCGA-24-1104 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
       63.55         6.31         7.82         7.99         0.76         6.25 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        6.02         4.83        19.17        18.67        43.53         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14       105.99         9.11         1.18        22.22 
TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       26.96        16.21        56.58        70.62        39.88        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 
       44.09        45.50        25.87        10.26        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
       38.24         8.32         3.81        11.28         5.52         9.80 
TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        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        53.95        18.48 
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-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-25-1313 TCGA-25-1314 
       44.61         0.82        67.36        33.11        26.96        32.02 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       37.02         1.02        34.98        65.00        36.95        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 TCGA-25-1634 
       12.00         2.96        15.81         0.36        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       51.22        14.96        24.99        18.05        85.05         1.02 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 
        3.02        45.01        19.99        42.02        29.03        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1701 
       26.99        44.71        47.18       101.79         0.79        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       18.67        59.67        18.25        41.98        29.23        34.62 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 
       17.00        66.81        62.93        39.12        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       17.33        12.36        12.30         7.23         5.36        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        45.11         4.90        42.25        11.84 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       11.47         9.76        21.04        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 
        2.47        15.68         0.26        48.10        44.91         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-31-1953 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 
       36.62         1.22         6.71        44.12         2.20        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       21.53        22.85        30.08        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       35.05        18.31        20.52        14.17        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2593 TCGA-57-1582 
       26.04        23.74         9.44        42.02         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 
       11.38        21.14         1.74        22.32        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
      116.12         9.40         2.14        44.81        20.52         8.09 
TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 
       20.94        27.88         4.34        31.79        28.47        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
        2.43        33.67        43.69         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 
       13.02         9.07        34.13        31.30        42.51        56.61 
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-61-2018 TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2097 
       30.64        45.40         4.77        51.72        58.39        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2111 TCGA-61-2612 
       65.52        55.50         6.48        76.87       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56P TCGA-WR-A838 
        8.61        39.68         8.05 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 
        1.81        49.15         2.01        21.57        63.98        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       76.57        71.47        82.39        48.89        27.88        28.64 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 TCGA-09-1675 TCGA-09-2044 
       89.33        74.93        57.60        30.51        97.55         6.12 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2053 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
        4.54        71.11        39.75        25.91        81.47        18.51 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 TCGA-13-0758 
       15.12         6.21        44.55        12.39         2.50        11.38 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0801 TCGA-13-0804 
       31.04        21.40        36.72        28.70         8.28        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0903 
       35.28       107.18        74.27        66.67        61.84        47.38 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0924 
       44.94        44.84        34.06        29.98        21.17         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1412 TCGA-13-1483 TCGA-13-1491 
       10.88         6.61         7.36         5.33        29.42        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-2071 
       73.55        38.20        13.97        32.84         4.77         6.28 
TCGA-13-A5FT TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1023 
       54.77        72.20        27.52        16.70         2.93        40.54 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
       31.76        49.41         8.81        29.13         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1120 
       54.51         3.22        31.20         4.57        86.01         4.27 
TCGA-23-1122 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 
       39.09        87.48        91.66        77.00         2.76         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 
       11.64        21.80         7.66        54.12        47.41         6.38 
TCGA-24-1419 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1463 
        7.86         5.95         5.36        17.39        28.37        72.92 
TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
        3.45        57.40        64.27        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1563 TCGA-24-1567 TCGA-24-1603 TCGA-24-1843 
       58.09        88.50        47.70        17.23        90.15         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2035 
        3.72         4.37         5.79        22.68        16.44        28.18 
TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 
       64.01        36.16         0.79        36.23        16.64        55.86 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1315 TCGA-25-1322 TCGA-25-1623 TCGA-25-1625 
       53.26         1.02        51.06         2.99        18.58        18.02 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-2042 TCGA-25-2391 
       20.61         7.86         0.30        56.94        13.02        49.05 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2401 TCGA-29-1688 TCGA-29-1694 TCGA-29-1696 
       38.04        12.00         2.96        78.90        38.53        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1762 TCGA-29-1768 TCGA-29-1769 
       31.20        68.32         0.53        85.68        31.23        22.98 
TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 TCGA-29-2427 TCGA-30-1861 TCGA-30-1880 
       11.84        14.93         8.38        62.47        34.78        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-31-1955 TCGA-36-1568 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       22.49        42.51        28.77        22.55         8.55        25.74 
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-36-2549 TCGA-3P-A9WA TCGA-42-2590 
       21.60         2.24        20.98         6.05         7.99         7.46 
TCGA-42-2591 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       40.77        29.00        25.08        80.12        22.32        34.39 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 
        5.42        11.11        31.43        18.54        48.79        44.84 
TCGA-61-1895 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 
        1.45        37.05        48.92        67.76        43.43         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2094 
        5.52        17.98         1.18        45.96         4.80        71.74 
TCGA-61-2095 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q 
       61.64        20.68        44.52        22.22        31.07        18.94 
TCGA-VG-A8LO 
        0.79 

  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                        107.18 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        26.96                         29.00 
[1] "0.3 - 180.2 (27.0)" "0.3 - 107.2 (29.0)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  2(1Q21.3) MUTATED         0   354                2
  AMP PEAK  2(1Q21.3) WILD-TYPE       2   203                0
D2V3, multiclass
                  clus
vv                 AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    354                           203
  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, continuous
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     2 361
  AMP PEAK  2(1Q21.3) WILD-TYPE   1 207
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      2  361
  AMP PEAK  2(1Q21.3) WILD-TYPE    1  207
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                            2                             1
  YES                         361                           207
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(1Q21.3) MUTATED   10 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                          10                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q21.3) MUTATED                                  2    11
  AMP PEAK  2(1Q21.3) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1Q21.3) MUTATED                          20
  AMP PEAK  2(1Q21.3) WILD-TYPE                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1Q21.3) MUTATED                                           1   305
  AMP PEAK  2(1Q21.3) WILD-TYPE                                         0   170
D2V7, multiclass
                                           clus
vv                                          AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                          20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             305
                                           clus
vv                                          AMP PEAK  2(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     6 201
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      6  201
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  124
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         201
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           124
[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   131 172
  AMP PEAK  3(1Q42.2) WILD-TYPE 135 118
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          303                           253 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                          172                           118 
$`AMP PEAK  3(1Q42.2) MUTATED`
TCGA-04-1331 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1356 TCGA-04-1364 
       40.24        18.51        65.52        63.09        49.28        33.67 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       56.55        19.99        38.37       119.08        84.20        55.43 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 
       64.64        31.86        47.70        45.37         9.47        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       35.57         9.99        38.43        57.60        61.87        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
       17.98         5.85         8.55         6.12        35.15         4.54 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 
      112.41        63.09        39.75        20.94        12.46        54.31 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       33.24        11.70         3.91        35.44        35.80        19.86 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       24.59        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 
       55.17         2.50        11.18        11.54        32.25        19.59 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0883 TCGA-13-0886 
        7.79         8.12         8.28         8.19        68.94        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 
       66.67        70.39        67.99        57.47        56.15        19.36 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 
       48.33        44.94        37.08        27.72        14.89         4.64 
TCGA-13-0923 TCGA-13-1403 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        6.41        10.88         5.92         6.84         4.70         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       54.64        87.06        98.04        20.68        22.39        70.82 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 TCGA-13-1504 TCGA-13-1511 TCGA-13-1512 
       49.25        54.31        37.61        16.57         3.91         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       14.24         8.61        10.78        54.77         8.42        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-23-1021 TCGA-23-1026 TCGA-23-1027 
       26.20        25.38        19.10        47.54        26.83        31.76 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       29.13        18.90        68.68        33.30        86.01       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        39.09        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2641 TCGA-23-2643 TCGA-24-0968 TCGA-24-0982 TCGA-24-1105 
      115.89         2.76         4.70        19.66        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        19.17         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        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1634 
        2.96        15.81         0.36        20.61         7.86        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 
       51.22        14.96        24.99        18.05        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 
       44.71       101.79         0.79        68.32        16.90        18.67 
TCGA-29-1703 TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       59.67        29.23        85.68        66.81        62.93        39.12 
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         4.90        11.84        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       21.04        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
       11.47         7.99        26.04        23.74        42.02         7.46 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
        1.48        11.38         1.74        22.32        25.08        25.02 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD 
       80.12       116.12         9.40         2.14        44.81        20.52 
TCGA-61-1722 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 
        8.09        18.54         4.34        31.79        28.47        44.84 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        2.43        33.67        43.69        13.02         9.07        34.13 
TCGA-61-1911 TCGA-61-1917 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       42.51        43.43        38.17         4.01        30.64        39.85 
TCGA-61-2016 TCGA-61-2088 TCGA-61-2092 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
        1.18         4.77        51.72        58.39        60.62        65.52 
TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2613 
       55.50         6.48        76.87        20.68       125.75        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
        8.61        39.68         0.79 

$`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        71.47        82.39        41.59        29.10        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-09-0364 TCGA-09-0366 TCGA-09-1662 
       27.88        28.64        36.23        29.16        57.76        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       74.93        41.62        30.51         3.02        97.55         6.18 
TCGA-09-2050 TCGA-09-2055 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       71.11        26.93        25.91        81.47        18.51        32.28 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0758 TCGA-13-0761 
       15.12         6.21        44.55        12.39        11.38        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       30.35         8.71        43.86        35.28        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 
      107.18        91.40        61.84        69.01        43.36        57.07 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       47.38        47.84        44.84        34.06        29.98        21.17 
TCGA-13-0920 TCGA-13-0924 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 
       13.81         6.08         6.61         7.36         6.05         4.21 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       61.71        29.42        82.88        52.44        73.55        38.20 
TCGA-13-1496 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
        4.24        38.40        13.97        32.84         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 
        4.77         4.18         2.56        12.23         8.75         6.28 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       23.05        72.20        27.52        16.70         2.93         2.66 
TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 TCGA-23-1032 
       42.54        40.54        15.39        49.41         8.81         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1120 
       51.35        54.51         3.22        31.20         4.57         4.27 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 
       87.48        91.66        77.00        49.84         4.50         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1417 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        7.82         5.95         5.36         4.83        17.39        28.37 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 
       18.67        43.53        72.92        45.14       105.99         3.45 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1563 
       22.22        57.40        41.06        51.91        88.50        47.70 
TCGA-24-1567 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1927 
       17.23         3.72         4.37        11.28         5.79        16.44 
TCGA-24-1928 TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       11.05        44.84       109.71        53.95        18.48        28.18 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2288 TCGA-24-2297 TCGA-25-1623 
       57.07        36.16         0.79         0.82        55.86        18.58 
TCGA-25-1625 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-2042 TCGA-25-2391 
       18.02         0.30        56.94        60.59        13.02        49.05 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1691 
       38.04        12.00        19.99         2.96        26.99        47.18 
TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1705 TCGA-29-1707 
       38.53        33.70        31.20         0.53        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 
       34.62        17.00        31.23        22.55        11.84        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2428 TCGA-29-2431 TCGA-29-2436 
        8.38         5.36        34.62        45.11        42.25         9.76 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1880 TCGA-30-1887 
        0.26        48.10        44.91        34.78        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-36-1570 TCGA-36-1574 TCGA-36-1575 
        6.71        42.51        44.12        21.53        22.55         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       25.74        27.85        33.01        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-42-2588 TCGA-42-2591 TCGA-57-1582 
       23.80        21.60        20.98         9.44        40.77        24.03 
TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 
       21.14        29.00       180.20        22.32        34.39         5.42 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 
       11.11        20.94        31.43        27.88        48.79        35.80 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1907 TCGA-61-1910 
        1.45         8.42         5.79        11.41        31.30        37.05 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       14.50        17.98        30.64        45.96        45.40         4.80 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56Q 
       71.74        61.64        44.52        22.22         6.35        18.94 
TCGA-WR-A838 
        8.05 

  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 
                       152.02                        180.20 
  AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE 
                        26.83                         28.70 
[1] "0.4 - 152.0 (26.8)" "0.3 - 180.2 (28.7)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  3(1Q42.2) MUTATED         2   303                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                                    2                             0
  OVARY                                    303                           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, continuous
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.2) MUTATED     1 314
  AMP PEAK  3(1Q42.2) WILD-TYPE   2 254
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.2) MUTATED      1  314
  AMP PEAK  3(1Q42.2) WILD-TYPE    2  254
     clus
vv    AMP PEAK  3(1Q42.2) MUTATED AMP PEAK  3(1Q42.2) WILD-TYPE
  NO                            1                             2
  YES                         314                           254
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  3(1Q42.2) MUTATED    9 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                           9                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1Q42.2) MUTATED                                  2     8
  AMP PEAK  3(1Q42.2) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1Q42.2) MUTATED                          17
  AMP PEAK  3(1Q42.2) WILD-TYPE                        15
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1Q42.2) MUTATED                                           1   261
  AMP PEAK  3(1Q42.2) WILD-TYPE                                         0   214
D3V7, multiclass
                                           clus
vv                                          AMP PEAK  3(1Q42.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             261
                                           clus
vv                                          AMP PEAK  3(1Q42.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               214
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q42.2) MUTATED     4 169
  AMP PEAK  3(1Q42.2) WILD-TYPE   6 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q42.2) MUTATED      4  169
  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                         169
                        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   118 122
  AMP PEAK  4(2P23.2) WILD-TYPE 148 168
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          240                           316 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                          122                           168 
$`AMP PEAK  4(2P23.2) MUTATED`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       49.15        18.51        63.09        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 TCGA-04-1525 TCGA-04-1646 TCGA-04-1655 
       32.52        33.67        82.39        38.37        27.88        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       29.16         9.47        57.76        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 
       38.43        41.62        61.87        17.98         5.85         8.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0927 
        6.18        35.15        63.09        39.75        20.94        81.47 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-13-0723 TCGA-13-0724 
       33.24        32.28        11.70        35.44        39.58         2.73 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 
       17.82        55.17        11.18        34.06        21.40        38.93 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 TCGA-13-0886 
       30.35         8.12         8.19        43.86       107.18        74.27 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       70.39        67.99        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0906 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-1403 
       19.36        44.94        29.98        14.89         4.64        10.88 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 
        7.36         6.05         5.92         6.84         5.33        87.06 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 
       49.25        54.31        16.57         4.21         4.41         3.91 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 
       14.24        12.23         8.61         6.28         8.42        23.05 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 
       27.52        19.10         2.93         2.66        47.54        15.39 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       49.41         8.81        68.68        33.30        86.01       129.96 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2645 
       39.09        58.13        24.95        87.48        91.66         4.50 
TCGA-24-0970 TCGA-24-0982 TCGA-24-1417 TCGA-24-1418 TCGA-24-1424 TCGA-24-1431 
       11.64        22.32         7.82         7.99         6.02        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
       18.67        43.53       105.99         9.11         1.18        22.22 
TCGA-24-1544 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1560 
       26.96        41.06        51.91        41.39        58.09        44.09 
TCGA-24-1563 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 TCGA-24-1847 
       47.70        88.37        48.33        38.24         3.81        11.28 
TCGA-24-1850 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2026 
        5.52        11.05         4.87       152.02        44.84        34.82 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 
       14.43        18.48         0.79         0.36        47.54        44.61 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-25-1312 TCGA-25-1315 TCGA-25-1317 
        0.82        67.36        33.11         1.02        51.06         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       34.98        65.00        36.95        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 
       18.02        15.81        20.61         7.86         0.30        35.54 
TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 
       14.96        18.05        85.05        49.05        38.04        12.00 
TCGA-25-2398 TCGA-25-2404 TCGA-25-2409 TCGA-29-1691 TCGA-29-1698 TCGA-29-1701 
       45.01        29.03        26.99        47.18        68.32        16.90 
TCGA-29-1702 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1770 
       18.67        34.62        17.00        66.81        62.93        24.36 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 
       17.33        12.36        14.93         8.38         5.36        65.00 
TCGA-29-2429 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1859 TCGA-30-1862 
        4.90        21.04        38.07        36.26        48.10         6.12 
TCGA-30-1867 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
        1.22        30.18        18.77         6.71        42.51         2.20 
TCGA-36-1568 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 
       28.77        22.85         8.55        30.08        24.69        35.05 
TCGA-36-2530 TCGA-36-2538 TCGA-36-2543 TCGA-36-2544 TCGA-36-2549 TCGA-36-2552 
       33.01        25.08         2.24        20.98         6.05        11.47 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 
       23.74         9.44        42.02        11.38         1.74        22.32 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
       25.02       180.20         9.40        44.81        20.52         8.09 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1741 TCGA-61-1899 
       31.43        27.88         4.34        31.79        33.67         8.42 
TCGA-61-1900 TCGA-61-1903 TCGA-61-1906 TCGA-61-1913 TCGA-61-1918 TCGA-61-1919 
        5.79        13.02        34.13        48.92        15.75        38.17 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2009 TCGA-61-2088 TCGA-61-2097 
        5.52        14.50         4.01        39.85         4.77        60.62 
TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 
       65.52        55.50         6.48        76.87        20.68       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       22.22         6.35         8.61        39.68        18.94         8.05 

$`AMP PEAK  4(2P23.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81         2.01        46.62        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       65.52        48.76        65.46        44.32        76.57        71.47 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        19.99       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       55.43        48.89        28.64        64.64        36.23        31.86 
TCGA-04-1654 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
       47.70        89.33        74.93        57.60        55.36        30.51 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 
        3.02        97.55         6.12         4.54       112.41        71.11 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0934 
       26.93        12.46        54.31        25.91        18.51         3.91 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.80        15.12        19.86         6.21        24.59        44.55 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       12.39        31.10        15.19         2.50        11.38        11.54 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        31.04         8.45        36.72        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.71         7.79         8.28        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0903 
       68.94        91.40        66.67        61.84        69.01        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        47.84        44.84        37.08        27.72        34.06 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 TCGA-13-1410 
       21.17        13.81         6.41         6.08         6.61         4.70 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
        4.21        54.64        61.71        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 
        4.24        37.61        38.40        13.97        32.84         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        4.18         2.56         3.09        10.78         8.75        54.77 
TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 TCGA-23-1022 
       25.94        26.20        72.20        25.38        16.70        42.54 
TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       40.54        26.83        31.76        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1120 
       51.35        54.51         3.22        31.20         4.57         4.27 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 
        6.38        33.47         0.53       115.89        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 
        2.76         4.70         7.63        19.66        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        53.95        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        32.02        37.02        33.96 
TCGA-25-1322 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 
        2.99         0.36        56.94        60.59        51.22        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        44.71       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       33.70        31.20         0.53        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       29.23        85.68        39.12        31.23        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        34.62        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        11.84        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-3P-A9WA TCGA-42-2582 
       18.31        20.52        14.17        16.18         7.99        26.04 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1992 
        7.46        40.77         1.48        24.03        21.14        29.00 
TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
       25.08        80.12        22.32       116.12        34.39         2.14 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
        5.42        11.11        20.94        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 
       44.84        35.80         2.43        43.69         1.45        11.41 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 
        9.07        31.30        37.05        42.51        56.61        67.76 
TCGA-61-1917 TCGA-61-1995 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
       43.43         2.01        17.98        30.64        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2110 TCGA-61-2613 TCGA-VG-A8LO 
       58.39        44.52        31.07         0.79 

  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                        119.08 
  AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE 
                       24.050                        29.325 
[1] "0.3 - 180.2 (24.0)" "0.3 - 119.1 (29.3)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  4(2P23.2) MUTATED         0   241                1
  AMP PEAK  4(2P23.2) WILD-TYPE       2   316                1
D4V3, multiclass
                  clus
vv                 AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    241                           316
  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, continuous
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P23.2) MUTATED     1 245
  AMP PEAK  4(2P23.2) WILD-TYPE   2 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P23.2) MUTATED      1  245
  AMP PEAK  4(2P23.2) WILD-TYPE    2  323
     clus
vv    AMP PEAK  4(2P23.2) MUTATED AMP PEAK  4(2P23.2) WILD-TYPE
  NO                            1                             2
  YES                         245                           323
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(2P23.2) MUTATED    4 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                           4                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(2P23.2) MUTATED                                  1     8
  AMP PEAK  4(2P23.2) WILD-TYPE                                2    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(2P23.2) MUTATED                          15
  AMP PEAK  4(2P23.2) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(2P23.2) MUTATED                                           1   202
  AMP PEAK  4(2P23.2) WILD-TYPE                                         0   273
D4V7, multiclass
                                           clus
vv                                          AMP PEAK  4(2P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             202
                                           clus
vv                                          AMP PEAK  4(2P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               273
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P23.2) MUTATED     4 138
  AMP PEAK  4(2P23.2) WILD-TYPE   6 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P23.2) MUTATED      4  138
  AMP PEAK  4(2P23.2) WILD-TYPE    6  187
                        clus
vv                       AMP PEAK  4(2P23.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         138
                        clus
vv                       AMP PEAK  4(2P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           187
[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   111 140
  AMP PEAK  5(2Q31.2) WILD-TYPE 155 150
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          251                           305 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                          140                           150 
$`AMP PEAK  5(2Q31.2) MUTATED`
TCGA-04-1342 TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       18.51        48.76        63.98        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1649 
       33.67        41.59        19.99        29.10        84.20        64.64 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       31.86        45.37         9.47        57.76        17.98        35.57 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       38.43        89.33        41.62        55.36        17.98         5.85 
TCGA-09-1673 TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 
        3.02         6.18         4.54       112.41        71.11        39.75 
TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       81.47        11.70        35.44        19.86        24.59        39.58 
TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
        2.73        17.82        55.17        11.18        11.38        11.54 
TCGA-13-0762 TCGA-13-0800 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       32.25         8.12        43.86        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 
       66.67        70.39        69.01        43.36        19.36        47.38 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       48.33        44.94        44.84        21.17        14.89        13.81 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1488 TCGA-13-1495 TCGA-13-1496 
       87.06        61.71        29.42        70.82        49.25         4.24 
TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 
       54.31        32.84        16.57         4.21         4.41         2.56 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-20-0987 TCGA-20-1684 
        3.91        14.24         8.61         6.28        23.05        19.10 
TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 
       16.70        47.54        42.54        15.39        26.83        49.41 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1122 
       18.90         2.24         3.22        68.68        33.30        39.09 
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-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0982 TCGA-24-1418 
        2.76         4.70         4.50        19.66        22.32         7.99 
TCGA-24-1422 TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        0.76         5.95        17.39        28.37        18.67        43.53 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
        8.55        45.14       105.99         9.11         1.18        22.22 
TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       26.96        64.27        16.21        58.09        70.62        39.88 
TCGA-24-1560 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       44.09        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 
        3.81         5.52         9.80        30.21        11.05        81.11 
TCGA-24-2020 TCGA-24-2030 TCGA-24-2033 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
      152.02        53.95        18.48         0.79         0.36        47.54 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 TCGA-24-2298 
       70.45        44.61         0.82        67.36        33.11        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 
        1.02        26.96        32.02         1.02        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1626 TCGA-25-1630 TCGA-25-1634 TCGA-25-1870 
       33.96         2.99        15.81         7.86        35.54        14.96 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
       18.05        85.05        13.02         1.02         3.02        12.00 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-29-1688 TCGA-29-1691 TCGA-29-1694 
       45.01        42.02         2.96        78.90        47.18        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 
        0.79        33.70        68.32        18.67        18.25        41.98 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 
       17.00        66.81        62.93        39.12        22.98        24.36 
TCGA-29-1775 TCGA-29-1781 TCGA-29-1783 TCGA-29-2425 TCGA-29-2429 TCGA-29-2432 
       12.36         8.38         7.23        65.00         4.90        11.84 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1862 
       11.47        38.07        51.91         2.47        48.10         6.12 
TCGA-30-1866 TCGA-31-1950 TCGA-31-1951 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       36.62        18.77        22.49         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2544 TCGA-36-2547 
       27.85        24.69        33.01        29.82        20.98        20.52 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
       16.18        11.47        23.74        40.77         1.48        24.03 
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-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.52         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 
       76.87        22.22         6.35        39.68        18.94 

$`AMP PEAK  5(2Q31.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1365 
       11.87        65.52        63.09        21.57        65.46        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 
       71.47        82.39        56.55        38.37       119.08        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
       48.89        27.88        28.64        36.23        47.70        29.16 
TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1674 
        9.99        74.93        57.60        61.87        30.51         8.55 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 
       97.55         6.12        35.15        63.09        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       12.46        54.31        25.91        18.51        33.24        32.28 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 
        3.91        35.80        15.12         6.21        44.55        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       31.10        15.19         2.50        34.06        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
        8.71         7.79         8.28         8.19        35.28        35.28 
TCGA-13-0807 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 
       13.61        74.27        61.84        67.99        57.47        56.15 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       57.07        47.84        37.08        27.72        34.06        29.98 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1412 
        4.64         6.41         6.08        10.88         7.36         5.33 
TCGA-13-1477 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       54.64        98.04        20.68        22.39        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1507 
       73.55        38.20        37.61        38.40        13.97         4.77 
TCGA-13-1509 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        4.18         3.09        12.23        10.78         8.75        54.77 
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-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
        2.93         2.66        40.54        31.76         8.81        29.13 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       51.35        54.51        31.20         4.57        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-24-0966 
        4.27         6.38        87.48        91.66        49.84         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56         7.66        54.12        63.55 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 TCGA-24-1423 
       47.41         6.31         6.38         7.82         7.86         6.25 
TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 
        6.02         5.36         4.83        19.17        72.92        12.46 
TCGA-24-1470 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
        3.45        57.40        56.58        41.06        51.91        41.39 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       88.50        19.53        45.50        47.70        25.87        10.26 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
       17.23        90.15        48.33         4.37        11.28         5.79 
TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       22.68        16.44         4.87        44.84        58.16        34.82 
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-24-2260 TCGA-24-2271 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1315 
       36.16        31.63        36.23        16.64        55.86        51.06 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       37.02        34.98        12.00         2.96        18.58        18.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
        0.36        20.61         0.30        56.94        60.59        51.22 
TCGA-25-1871 TCGA-25-2391 TCGA-25-2393 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 
       24.99        49.05        38.04        19.99        29.03        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1693 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 
       26.99        44.71       101.79        31.20         0.53        16.90 
TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 
       59.67        29.23        34.62        85.68        31.23        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1784 TCGA-29-1785 
       17.33        11.84        12.30        14.93         5.36        34.62 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        62.47        45.11        42.25         9.76        21.04 
TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1867 
       36.26        15.68         0.26        44.91        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-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
        6.71        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 
       21.53        22.85        22.55        24.23        35.05        29.49 
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-36-2548 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       14.17         6.05         7.99        26.04         9.44        42.02 
TCGA-42-2590 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 
        7.46        21.14        29.00        25.08        80.12        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
      116.12        34.39         2.14         5.42        44.81        11.11 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       31.43        18.54        27.88        48.79        44.84        35.80 
TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1911 TCGA-61-1913 
        1.45        11.41        13.02         9.07        42.51        48.92 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       56.61        43.43        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       17.98        39.85         1.18        45.96         4.80        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 TCGA-61-2109 TCGA-61-2110 
       71.74        61.64        58.39        65.52        20.68        44.52 
TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO TCGA-WR-A838 
      125.75        31.07         8.61         0.79         8.05 

  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                        129.96 
  AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE 
                        24.95                         29.10 
[1] "0.4 - 180.2 (24.9)" "0.3 - 130.0 (29.1)"
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  5(2Q31.2) MUTATED         0   252                1
  AMP PEAK  5(2Q31.2) WILD-TYPE       2   305                1
D5V3, multiclass
                  clus
vv                 AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    252                           305
  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, continuous
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q31.2) MUTATED     3 256
  AMP PEAK  5(2Q31.2) WILD-TYPE   0 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED      3  256
  AMP PEAK  5(2Q31.2) WILD-TYPE    0  312
     clus
vv    AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  NO                            3                             0
  YES                         256                           312
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  5(2Q31.2) MUTATED    4 10  2  1
  AMP PEAK  5(2Q31.2) WILD-TYPE 10 16  3  2
D5V6, multiclass
    clus
vv   AMP PEAK  5(2Q31.2) MUTATED AMP PEAK  5(2Q31.2) WILD-TYPE
  R0                           4                            10
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(2Q31.2) MUTATED                                  2     8
  AMP PEAK  5(2Q31.2) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(2Q31.2) MUTATED                          13
  AMP PEAK  5(2Q31.2) WILD-TYPE                        19
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(2Q31.2) MUTATED                                           1   221
  AMP PEAK  5(2Q31.2) WILD-TYPE                                         0   254
D5V7, multiclass
                                           clus
vv                                          AMP PEAK  5(2Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               8
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             221
                                           clus
vv                                          AMP PEAK  5(2Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               254
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(2Q31.2) MUTATED     6 139
  AMP PEAK  5(2Q31.2) WILD-TYPE   4 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(2Q31.2) MUTATED      6  139
  AMP PEAK  5(2Q31.2) WILD-TYPE    4  186
                        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                           186
[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   227 238
  AMP PEAK  6(3Q26.2) WILD-TYPE  39  52
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          465                            91 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                          238                            52 
$`AMP PEAK  6(3Q26.2) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 
      119.08        29.10        84.20        48.89        27.88        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-10-0928 
        4.54       112.41        71.11        63.09        39.75        18.51 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       33.24        11.70         3.91        35.44        35.80        15.12 
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        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       38.93        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 
        8.12         8.28         8.19        43.86        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       67.99        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0919 
       48.33        44.94        44.84        37.08        27.72        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         4.64         6.41        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       87.06        29.42        98.04        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 
        4.77         4.18         2.56         3.91         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       12.23         8.61        10.78         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        8.42        23.05        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        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       29.13        18.90         2.24        51.35        54.51        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       68.68         4.57        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        6.38        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-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 
        4.70         4.50        19.66        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 
       19.17        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 
       53.95        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         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       56.94        35.54        51.22        14.96        24.99        18.05 
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        47.18       101.79        38.53 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
        0.79        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       59.67        18.25        29.23        34.62        17.00        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 
       62.93        39.12        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        34.62        65.00 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ 
       45.11         4.90        42.25        11.84        11.47        21.04 
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-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       14.17        16.18        11.47         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       21.14         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-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       44.81        20.52         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       27.88        31.79        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-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 
       56.61        67.76        43.43        15.75        38.17         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50         4.01        30.64        39.85        30.64         1.18 
TCGA-61-2087 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
        4.80        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-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

$`AMP PEAK  6(3Q26.2) WILD-TYPE`
TCGA-04-1351 TCGA-04-1638 TCGA-04-1648 TCGA-09-1664 TCGA-09-1675 TCGA-09-2054 
       65.46        55.43        28.64        74.93        97.55        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 
       26.93        12.46        54.31        25.91        81.47        32.28 
TCGA-10-0938 TCGA-13-0720 TCGA-13-0799 TCGA-13-0805 TCGA-13-0883 TCGA-13-0891 
       19.86        44.55         7.79        35.28        68.94        69.01 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0924 
       47.38        47.84        34.06        29.98        21.17         6.08 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1500 TCGA-20-0996 TCGA-23-1111 
       54.64        61.71        20.68        13.97        72.20         3.22 
TCGA-24-0966 TCGA-24-0975 TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1425 
        7.63        21.80        54.12        47.41         6.38         5.95 
TCGA-24-1430 TCGA-24-1464 TCGA-24-1546 TCGA-24-1560 TCGA-24-1565 TCGA-24-1603 
       28.37        12.46        64.27        44.09        10.26        90.15 
TCGA-24-1846 TCGA-24-2024 TCGA-24-2029 TCGA-24-2035 TCGA-25-1314 TCGA-25-1315 
        4.37        58.16        14.43        28.18        32.02        51.06 
TCGA-25-1316 TCGA-25-1633 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 
       37.02        60.59        13.02         1.02        38.04        12.00 
TCGA-25-2401 TCGA-25-2408 TCGA-29-1690 TCGA-29-1696 TCGA-29-1707 TCGA-29-1762 
        2.96        31.00        44.71        33.70        41.98        85.68 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1781 TCGA-29-2414 TCGA-29-2427 
       31.23        22.55        17.33         8.38        86.17        62.47 
TCGA-29-2436 TCGA-30-1880 TCGA-31-1955 TCGA-36-1571 TCGA-36-2537 TCGA-36-2540 
        9.76        57.57        42.51        22.85        25.91        23.80 
TCGA-36-2549 TCGA-57-1583 TCGA-59-2349 TCGA-59-2363 TCGA-61-1721 TCGA-61-1730 
        6.05        11.38        80.12         5.42        11.11         4.34 
TCGA-61-1734 TCGA-61-1743 TCGA-61-1995 TCGA-61-2002 TCGA-61-2017 TCGA-61-2018 
       28.47        43.69         2.01        17.98        45.96        45.40 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2110 
        4.77        51.72        61.64        58.39        55.50        44.52 
TCGA-WR-A838 
        8.05 

  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                         0.26                          1.02 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                       180.20                         97.55 
  AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE 
                        26.96                         31.23 
[1] "0.3 - 180.2 (27.0)" "1.0 - 97.5 (31.2)" 
[1] "hr=" "1"  
D6V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  6(3Q26.2) MUTATED         2   465                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                                    2                             0
  OVARY                                    465                            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, continuous
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED     3 474
  AMP PEAK  6(3Q26.2) WILD-TYPE   0  94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      3  474
  AMP PEAK  6(3Q26.2) WILD-TYPE    0   94
     clus
vv    AMP PEAK  6(3Q26.2) MUTATED AMP PEAK  6(3Q26.2) WILD-TYPE
  NO                            3                             0
  YES                         474                            94
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  6(3Q26.2) MUTATED   11 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                          11                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(3Q26.2) MUTATED                                  2    16
  AMP PEAK  6(3Q26.2) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(3Q26.2) MUTATED                          25
  AMP PEAK  6(3Q26.2) WILD-TYPE                         7
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(3Q26.2) MUTATED                                           1   400
  AMP PEAK  6(3Q26.2) WILD-TYPE                                         0    75
D6V7, multiclass
                                           clus
vv                                          AMP PEAK  6(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              16
  BLACK OR AFRICAN AMERICAN                                          25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             400
                                           clus
vv                                          AMP PEAK  6(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                             7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(3Q26.2) MUTATED     8 277
  AMP PEAK  6(3Q26.2) WILD-TYPE   2  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(3Q26.2) MUTATED      8  277
  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                         277
                        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    65  87
  AMP PEAK  7(4P16.3) WILD-TYPE 201 203
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                          152                           404 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                           87                           203 
$`AMP PEAK  7(4P16.3) MUTATED`
TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 
       48.76        21.57        65.46        49.28        33.67        76.57 
TCGA-04-1530 TCGA-04-1646 TCGA-09-1666 TCGA-09-1668 TCGA-09-1675 TCGA-09-2048 
      119.08        27.88        57.60        55.36        97.55         4.54 
TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 
       26.93        54.31        25.91        35.80        15.12        24.59 
TCGA-13-0726 TCGA-13-0758 TCGA-13-0791 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 
       31.10        11.38        38.93         7.79         8.12         8.19 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0893 TCGA-13-0901 
       68.94       107.18        66.67        70.39        43.36        19.36 
TCGA-13-0905 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-1405 TCGA-13-1412 
       47.84        29.98        13.81         4.64         7.36         5.33 
TCGA-13-1481 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 
       87.06        38.20         4.24        54.31        38.40        32.84 
TCGA-13-1505 TCGA-13-2071 TCGA-13-A5FU TCGA-23-1026 TCGA-23-1032 TCGA-23-1109 
        4.21         6.28         8.42        26.83         2.24        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        51.06        36.95        33.96 
TCGA-25-1322 TCGA-25-1628 TCGA-25-1630 TCGA-25-1635 TCGA-25-1870 TCGA-25-1877 
        2.99        20.61         7.86        51.22        14.96        18.05 
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-29-1691 TCGA-29-1701 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       47.18        16.90        18.25        34.62        17.00        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1785 
       62.93        31.23        22.98        24.36        12.36        34.62 
TCGA-29-2429 TCGA-29-2431 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
        4.90        42.25        21.04        38.07        51.91         2.47 
TCGA-30-1866 TCGA-36-1569 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2543 
       36.62        29.10        27.85        35.05        33.01         2.24 
TCGA-36-2544 TCGA-36-2551 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       20.98        16.18         9.44        42.02         7.46        40.77 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-61-1722 TCGA-61-1724 
       24.03         1.74        25.08        25.02         8.09        20.94 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 
       27.88        31.79        35.80         2.43        43.69         5.79 
TCGA-61-1907 TCGA-61-1915 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 TCGA-61-2094 
       31.30        67.76        15.75        39.85        30.64        71.74 
TCGA-61-2102 TCGA-61-2614 
        6.48         8.61 

$`AMP PEAK  7(4P16.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1350 TCGA-04-1361 
       18.51        11.87        65.52        63.09        63.98        32.52 
TCGA-04-1362 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 
       44.32        71.47        82.39        56.55        41.59        19.99 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       38.37        29.10        84.20        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
        9.47        57.76        17.98        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        41.62        61.87        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-09-2049 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-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       81.47        18.51        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       35.44        19.86         6.21        44.55        39.58         2.73 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       12.39        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.54        34.06        32.25        31.04        21.40         8.45 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 
       36.72        28.70        30.35        19.59         8.71         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 
       43.86        35.28        35.28        13.61        91.40        74.27 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       61.84        67.99        69.01        57.47        56.15        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       34.06        21.17        14.89         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       54.64        61.71        29.42        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1498 
       70.82        82.88        52.44        73.55        49.25        37.61 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       13.97        16.57         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        3.91         3.09        14.24        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
        8.75        54.77        23.05        25.94        26.20        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-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 
       47.54        42.54        40.54        15.39        31.76        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
        8.81        29.13        18.90         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1809 
       33.30        86.01       129.96         4.27         6.38         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 
       24.95        87.48        77.00        49.84         2.76         4.50 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        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-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.36         4.83        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       72.92        45.14       105.99         9.11         3.45         1.18 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 
       64.27        16.21        56.58        51.91        41.39        88.50 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1614 
       44.09        45.50        25.87        10.26        17.23        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 
       38.24         8.32        11.28         5.52        22.68        30.21 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
      109.71        14.43        53.95        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
        0.79         0.36        47.54        31.63        44.61         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 
       36.23        16.64        53.26         1.02        32.02        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
        1.02        34.98        65.00        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       18.02        15.81         0.36         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2399 TCGA-25-2400 
       35.54        24.99        85.05        13.02        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        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 
        0.53        18.67        59.67        41.98        29.23        85.68 
TCGA-29-1766 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 
       39.12        22.55        17.33        11.84        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23         5.36        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-30-1853 TCGA-30-1856 
       45.11        11.84        11.47         9.76        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 
        0.26        48.10        44.91        34.78         6.12         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-31-1953 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-36-1570 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-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 
       25.74        24.23        24.69        29.49        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.08        23.80        21.60        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2593 
        6.05        11.47         7.99        26.04        23.74         1.48 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 
       11.38        21.14        22.32        29.00       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-59-A5PD TCGA-61-1721 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       44.81        20.52        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 
        0.79         8.05 

  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                         1.02                          0.26 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       119.08                        180.20 
  AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE 
                       29.540                        26.595 
[1] "1.0 - 119.1 (29.5)" "0.3 - 180.2 (26.6)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  7(4P16.3) MUTATED         0   153                1
  AMP PEAK  7(4P16.3) WILD-TYPE       2   404                1
D7V3, multiclass
                  clus
vv                 AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    153                           404
  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, continuous
D7V5, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED     2 156
  AMP PEAK  7(4P16.3) WILD-TYPE   1 412
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      2  156
  AMP PEAK  7(4P16.3) WILD-TYPE    1  412
     clus
vv    AMP PEAK  7(4P16.3) MUTATED AMP PEAK  7(4P16.3) WILD-TYPE
  NO                            2                             1
  YES                         156                           412
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  7(4P16.3) MUTATED    3  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                           3                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(4P16.3) MUTATED                                  0     6
  AMP PEAK  7(4P16.3) WILD-TYPE                                3    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(4P16.3) MUTATED                          12
  AMP PEAK  7(4P16.3) WILD-TYPE                        20
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(4P16.3) MUTATED                                           0   128
  AMP PEAK  7(4P16.3) WILD-TYPE                                         1   347
D7V7, multiclass
                                           clus
vv                                          AMP PEAK  7(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             128
                                           clus
vv                                          AMP PEAK  7(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               347
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(4P16.3) MUTATED     3  86
  AMP PEAK  7(4P16.3) WILD-TYPE   7 239
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(4P16.3) MUTATED      3   86
  AMP PEAK  7(4P16.3) WILD-TYPE    7  239
                        clus
vv                       AMP PEAK  7(4P16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       AMP PEAK  7(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           239
[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    54  57
  AMP PEAK  8(4Q13.3) WILD-TYPE 212 233
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                          111                           445 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                           57                           233 
$`AMP PEAK  8(4Q13.3) MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 
       41.00        46.62        63.09        21.57        65.46        49.28 
TCGA-04-1362 TCGA-04-1525 TCGA-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-09-1665 
       44.32        38.37        55.43        27.88        31.86        41.62 
TCGA-09-1674 TCGA-10-0936 TCGA-10-0938 TCGA-13-0764 TCGA-13-0791 TCGA-13-0792 
        8.55        35.80        19.86        31.04        38.93        36.72 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0802 TCGA-13-0883 TCGA-13-0904 
       30.35         8.71         7.79         8.19        68.94        48.33 
TCGA-13-0920 TCGA-13-1408 TCGA-13-1410 TCGA-13-1483 TCGA-13-1495 TCGA-13-1499 
       13.81         5.92         4.70        29.42        49.25        38.40 
TCGA-13-1504 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-1685 TCGA-20-1686 
       16.57         8.61         6.28         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         4.57        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        56.94        51.22        13.02         3.02 
TCGA-25-2400 TCGA-29-1691 TCGA-29-1701 TCGA-29-1702 TCGA-29-1761 TCGA-29-1764 
       42.02        47.18        16.90        18.67        17.00        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        11.84        21.04 
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-59-A5PD TCGA-61-1722 TCGA-61-1728 TCGA-61-1743 TCGA-61-1914 TCGA-61-1915 
       20.52         8.09        27.88        43.69        56.61        67.76 
TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2008 TCGA-61-2012 TCGA-61-2101 
       43.43        15.75        14.50        30.64        30.64        55.50 
TCGA-61-2104 TCGA-61-2614 TCGA-VG-A8LO 
       76.87         8.61         0.79 

$`AMP PEAK  8(4Q13.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 
       65.52        48.76        63.98        32.52        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 
       71.47        82.39        56.55        41.59        19.99       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       29.10        84.20        48.89        28.64        64.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       35.57         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       54.31        25.91        81.47        18.51        33.24        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 
       11.70         3.91        35.44        15.12         6.21        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        31.10        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-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 TCGA-13-0795 
       34.06        32.25        21.40         8.45        28.70        19.59 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28        43.86        35.28        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
      107.18        91.40        74.27        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 
       27.72        34.06        29.98        21.17        14.89         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        6.84         4.21         5.33        54.64        87.06        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       98.04        20.68        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 
       73.55        38.20         4.24        54.31        37.61        13.97 
TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       32.84         4.21         4.41         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        3.91         3.09        14.24        12.23        10.78         8.75 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
       54.77        23.05        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       25.38        19.10         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        54.51         3.22        31.20 
TCGA-23-1119 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
      129.96        39.09        58.13         0.53        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-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
        7.63        19.66        11.64        21.80         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 
       54.12        63.55        47.41         6.31         7.82         7.99 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 
        0.76         6.25         6.02         5.95         5.36        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       19.17        18.67        43.53         8.55        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-24-1546 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-24-1560 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-24-1843 
       25.87        10.26        17.23        90.15        88.37         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.81         4.37         5.79         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
       16.44        81.11         4.87       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        53.95        18.48        64.01        44.52 
TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       57.07         0.36        31.63        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 
       67.36        36.23        16.64        55.86         1.02        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 
       15.81         0.36        20.61         7.86         0.30        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 
       35.54        14.96        24.99        18.05        85.05        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
        1.02        38.04        12.00        45.01        19.99         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        44.71       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       38.53         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       59.67        18.25        41.98        29.23        34.62        85.68 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 
       66.81        39.12        31.23        22.98        22.55        17.33 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 
       11.84        12.30         8.38         7.23        34.62        86.17 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       65.00        62.47        45.11         4.90        42.25        11.47 
TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        9.76        38.07        36.26        15.68         0.26        48.10 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       44.91        34.78         6.12         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-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       42.51        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 
       22.55         8.55        30.08        25.74        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-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
        6.05        11.47         7.99        26.04        23.74         9.44 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1586 
       42.02         7.46        40.77         1.48        21.14        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08       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-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        18.54         4.34        31.79        28.47 
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-61-1919 TCGA-61-1995 
       31.30        37.05        42.51        48.92        38.17         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 
        5.52        17.98         4.01        39.85         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-61-2109 TCGA-61-2110 
       58.39        60.62        65.52         6.48        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-WR-A838 
        8.05 

  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 
                         88.5                         180.2 
  AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE 
                        27.88                         28.47 
[1] "0.8 - 88.5 (27.9)"  "0.3 - 180.2 (28.5)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK  8(4Q13.3) MUTATED         0   111                1
  AMP PEAK  8(4Q13.3) WILD-TYPE       2   446                1
D8V3, multiclass
                  clus
vv                 AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    111                           446
  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, continuous
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED     1 112
  AMP PEAK  8(4Q13.3) WILD-TYPE   2 456
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED      1  112
  AMP PEAK  8(4Q13.3) WILD-TYPE    2  456
     clus
vv    AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  NO                            1                             2
  YES                         112                           456
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  8(4Q13.3) MUTATED    0  4  2  0
  AMP PEAK  8(4Q13.3) WILD-TYPE 14 22  3  3
D8V6, multiclass
    clus
vv   AMP PEAK  8(4Q13.3) MUTATED AMP PEAK  8(4Q13.3) WILD-TYPE
  R0                           0                            14
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(4Q13.3) MUTATED                                  1     6
  AMP PEAK  8(4Q13.3) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(4Q13.3) MUTATED                           6
  AMP PEAK  8(4Q13.3) WILD-TYPE                        26
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(4Q13.3) MUTATED                                           0    93
  AMP PEAK  8(4Q13.3) WILD-TYPE                                         1   382
D8V7, multiclass
                                           clus
vv                                          AMP PEAK  8(4Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              93
                                           clus
vv                                          AMP PEAK  8(4Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               382
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(4Q13.3) MUTATED     1  59
  AMP PEAK  8(4Q13.3) WILD-TYPE   9 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(4Q13.3) MUTATED      1   59
  AMP PEAK  8(4Q13.3) WILD-TYPE    9  266
                        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                           266
[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   147 149
  AMP PEAK  9(5P15.33) WILD-TYPE 119 141
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           296                            260 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                           149                            141 
$`AMP PEAK  9(5P15.33) MUTATED`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1346 TCGA-04-1349 TCGA-04-1350 
       40.24         2.01        18.51        65.52        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        71.47        56.55 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1654 
       19.99       119.08        84.20        27.88        64.64        47.70 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       41.62        57.60        17.98         3.02         8.55        97.55 
TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 
        6.18         6.12        35.15       112.41        71.11        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       20.94        12.46        81.47        33.24        32.28        11.70 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       35.80        15.12        39.58        12.39        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       55.17        11.18        11.54        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0801 TCGA-13-0802 
       36.72        28.70        30.35        19.59         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       43.86        35.28        68.94       107.18        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 
       61.84        67.99        43.36        56.15        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 TCGA-13-0920 TCGA-13-0923 
       48.33        47.84        44.94        27.72        13.81         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         6.61         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 
        4.21        87.06        98.04        70.82        82.88        73.55 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       49.25         4.24        54.31        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 
        4.41         4.77         4.18         2.56         3.09         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       10.78         8.75        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1024 
       26.20        27.52        25.38        16.70         2.93        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1032 TCGA-23-1111 
       26.83        31.76        49.41         8.81         2.24         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       68.68         4.57        86.01       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 
       39.09        58.13         0.53        91.66        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 
        4.70         4.50        19.66        21.80        41.56        22.32 
TCGA-24-1103 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1423 
       54.12         6.31         7.82         7.99         7.86         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        6.02         5.95         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
       43.53         8.55        72.92        45.14       105.99         9.11 
TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1549 TCGA-24-1552 TCGA-24-1553 
        1.18        26.96        57.40        56.58        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       88.50        70.62        39.88        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
       38.24         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-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 
       34.82        53.95        18.48        28.18        57.07        36.16 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 
       47.54        70.45        44.61         0.82        67.36        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 
       33.11        55.86        53.26        34.98        65.00        33.96 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
        2.99         2.96        18.58         0.36         7.86         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 
       56.94        35.54        14.96        18.05         1.02        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
        3.02        45.01        29.03        78.90        47.18       101.79 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
        0.79        33.70        31.20        17.00        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1777 
       39.12        31.23        22.98        24.36        17.33        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-30-1718 
        8.38         5.36        65.00        45.11        11.84        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1860 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 
       36.26         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        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       23.74         9.44         7.46         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-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1733 
       34.39        20.52        20.94        31.43        27.88        31.79 
TCGA-61-1738 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1914 
       35.80         8.42        11.41        13.02        34.13        56.61 
TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
       43.43        15.75        38.17         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2098 TCGA-61-2101 TCGA-61-2111 TCGA-61-2612 
       30.64         4.80        65.52        55.50       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56P 
        8.61        39.68 

$`AMP PEAK  9(5P15.33) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1347 
       41.00         1.81        49.15        46.62        11.87        63.09 
TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 
       48.76        65.46        32.52        82.39        41.59        38.37 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 
       29.10        55.43        48.89        28.64        36.23        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 
       45.37        29.16         9.47        74.93        61.87        55.36 
TCGA-09-1669 TCGA-09-1672 TCGA-09-2048 TCGA-09-2051 TCGA-09-2055 TCGA-10-0925 
       30.51         5.85         4.54        63.09        26.93        54.31 
TCGA-10-0926 TCGA-10-0928 TCGA-10-0934 TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 
       25.91        18.51         3.91        35.44        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 TCGA-13-0755 TCGA-13-0758 
       24.59        44.55         2.73        31.10         2.50        11.38 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       34.06        32.25        31.04         8.71         7.79         8.12 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0885 TCGA-13-0888 TCGA-13-0891 TCGA-13-0897 
       35.28        13.61        91.40        70.39        69.01        57.47 
TCGA-13-0900 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       57.07        44.84        37.08        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       14.89         4.64         7.36         4.70         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1494 
       61.71        29.42        20.68        22.39        52.44        38.20 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 
       37.61        38.40        13.97         3.91        14.24        12.23 
TCGA-13-2071 TCGA-20-0996 TCGA-20-1684 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 
        6.28        72.20        19.10         2.66        47.54        42.54 
TCGA-23-1023 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 
       40.54        29.13        18.90        51.35        54.51        31.20 
TCGA-23-1117 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
       33.30        33.47        24.95       115.89        87.48        77.00 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0980 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
        7.63        11.64         7.66        63.55        47.41         6.38 
TCGA-24-1422 TCGA-24-1426 TCGA-24-1430 TCGA-24-1464 TCGA-24-1470 TCGA-24-1474 
        0.76         5.36        28.37        12.46         3.45        22.22 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1558 TCGA-24-1560 
       64.27        16.21        41.06        51.91        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1842 
       45.50        47.70        25.87        10.26        17.23         8.32 
TCGA-24-1843 TCGA-24-1846 TCGA-24-1849 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 
        3.48         4.37         5.79        16.44        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2036 TCGA-24-2038 TCGA-24-2261 TCGA-24-2262 
      109.71        14.43        64.01        44.52         0.79         0.36 
TCGA-24-2271 TCGA-24-2290 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       31.63        36.23         1.02        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 
       37.02         1.02        36.95        12.00        18.02        15.81 
TCGA-25-1628 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       20.61        60.59        51.22        24.99        85.05        13.02 
TCGA-25-2391 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 
       49.05        12.00        19.99        42.02         2.96        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       26.99        44.71        38.53        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       18.67        59.67        18.25        41.98        29.23        34.62 
TCGA-29-1762 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 
       85.68        22.55        12.36        11.84        14.93         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       34.62        86.17        62.47         4.90        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
        9.76        21.04        38.07        15.68         0.26        48.10 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 
       34.78         6.12         1.22        57.57        48.79        45.57 
TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1570 TCGA-36-1571 
       30.18         6.71        42.51        44.12        21.53        22.85 
TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 
       22.55         8.55        25.74        24.23        33.01        29.49 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2545 TCGA-36-2549 TCGA-3P-A9WA 
       29.82        25.91        23.80        18.31         6.05         7.99 
TCGA-42-2589 TCGA-42-2591 TCGA-57-1584 TCGA-57-1586 TCGA-59-2349 TCGA-59-2350 
       42.02        40.77        21.14        22.32        80.12        22.32 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 
        9.40         2.14         5.42        44.81        11.11         8.09 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       18.54         4.34        28.47        48.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1904 TCGA-61-1907 
       33.67        43.69         1.45         5.79         9.07        31.30 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 
       37.05        42.51        48.92        67.76         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 
       14.50        17.98         1.18        45.96        45.40         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 
       51.72        71.74        61.64        58.39        60.62         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56Q 
       76.87        20.68        44.52        22.22        31.07        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  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                         115.89 
  AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE 
                        27.620                         29.115 
[1] "0.3 - 180.2 (27.6)" "0.3 - 115.9 (29.1)"
[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       1   259                0
D9V3, multiclass
                  clus
vv                 AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     298                            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"
D9V4, continuous
D9V5, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED     1 304
  AMP PEAK  9(5P15.33) WILD-TYPE   2 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      1  304
  AMP PEAK  9(5P15.33) WILD-TYPE    2  264
     clus
vv    AMP PEAK  9(5P15.33) MUTATED AMP PEAK  9(5P15.33) WILD-TYPE
  NO                             1                              2
  YES                          304                            264
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  9(5P15.33) MUTATED    4 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                            4                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(5P15.33) MUTATED                                  2     9
  AMP PEAK  9(5P15.33) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(5P15.33) MUTATED                          15
  AMP PEAK  9(5P15.33) WILD-TYPE                        17
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK  9(5P15.33) MUTATED                                           1
  AMP PEAK  9(5P15.33) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK  9(5P15.33) MUTATED     254
  AMP PEAK  9(5P15.33) WILD-TYPE   221
D9V7, multiclass
                                           clus
vv                                          AMP PEAK  9(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              254
                                           clus
vv                                          AMP PEAK  9(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                221
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(5P15.33) MUTATED     6 169
  AMP PEAK  9(5P15.33) WILD-TYPE   4 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(5P15.33) MUTATED      6  169
  AMP PEAK  9(5P15.33) WILD-TYPE    4  156
                        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                            156
[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   151 138
  AMP PEAK 10(6P22.3) WILD-TYPE 115 152
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          289                           267 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                          138                           152 
$`AMP PEAK 10(6P22.3) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
       40.24         1.81        18.51        65.52        63.09        48.76 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 
       21.57        65.46        44.32        33.67        82.39        41.59 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1651 TCGA-09-0364 
       38.37       119.08        29.10        84.20        36.23        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       57.76        17.98         9.99        38.43        89.33        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-2043 
       57.60        61.87        55.36        30.51         3.02         6.18 
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-10-0925 TCGA-10-0928 TCGA-10-0933 TCGA-10-0936 TCGA-13-0717 
       26.93        54.31        18.51        11.70        35.80        24.59 
TCGA-13-0724 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 
        2.73        55.17         2.50        11.18        11.54        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
       31.04        21.40        36.72        28.70        30.35        19.59 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0883 TCGA-13-0885 
        7.79         8.12         8.28        43.86        68.94        91.40 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0900 TCGA-13-0901 
       74.27        70.39        67.99        69.01        57.07        19.36 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 
       47.38        47.84        13.81         6.41         6.08         6.61 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        6.05         5.92         6.84         4.21         5.33        54.64 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       87.06        29.42        98.04        22.39        70.82        82.88 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 
       38.20         4.24        54.31        37.61        38.40         4.21 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        2.56        14.24        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        6.28        54.77        25.94        26.20        27.52        25.38 
TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 
       16.70         2.93         2.66        42.54        40.54        31.76 
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-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
       68.68         4.57        33.30       129.96         4.27         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       39.09        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2641 TCGA-23-2643 TCGA-24-0968 TCGA-24-0982 TCGA-24-1413 TCGA-24-1417 
        2.76         4.70        19.66        22.32         6.31         7.82 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.25         6.02         5.95        17.39        28.37        19.17 
TCGA-24-1435 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1551 
       43.53        12.46         9.11         3.45        22.22        51.91 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 
       58.09        88.50        70.62        19.53        47.70        25.87 
TCGA-24-1604 TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1920 TCGA-24-1927 
       88.37         3.48         3.81        11.28         9.80        16.44 
TCGA-24-2020 TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 
      152.02        34.82        53.95        18.48        64.01        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 
       36.16         0.79        47.54        44.61         0.82        16.64 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
        1.02        26.96        32.02         1.02        34.98        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 
       33.96         2.99        12.00         0.36         7.86        35.54 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 
       14.96        24.99        18.05        85.05         1.02        38.04 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-29-1691 
       12.00        45.01        42.02         2.96        29.03        47.18 
TCGA-29-1695 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1710 TCGA-29-1763 
        0.79        68.32        16.90        18.67        29.23        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1777 TCGA-29-1778 TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 TCGA-29-2432 
       12.30        14.93        86.17        65.00         4.90        11.84 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       21.04        38.07        51.91        36.26         2.47        15.68 
TCGA-30-1859 TCGA-30-1891 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       48.10        30.05        30.18         6.71        42.51         2.20 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 
       21.53        22.85        30.08        27.85        24.23        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 
       35.05        33.01        29.49        21.60         2.24        18.31 
TCGA-36-2547 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2593 
       20.52        11.47        26.04        23.74         9.44         1.48 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 
       24.03         1.74        22.32        25.08        25.02       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1730 
        9.40         2.14        44.81        20.52         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 
        8.05 

$`AMP PEAK 10(6P22.3) WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1350 
       41.00        49.15         2.01        46.62        11.87        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 
       49.28        32.52        76.57        71.47        56.55        19.99 
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-09-0365 TCGA-09-0369 TCGA-09-1664 TCGA-09-1670 
       47.70        45.37         9.47        35.57        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-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       25.91        81.47        33.24        32.28         3.91        35.44 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 
       15.12        19.86         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 
       31.10        15.19        17.82        11.38        34.06         8.45 
TCGA-13-0791 TCGA-13-0797 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       38.93         8.71         8.19        35.28        35.28        13.61 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0889 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
      107.18        66.67        61.84        43.36        57.47        56.15 
TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-1403 TCGA-13-1405 
       29.98        21.17        14.89         4.64        10.88         7.36 
TCGA-13-1410 TCGA-13-1482 TCGA-13-1485 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 
        4.70        61.71        20.68        52.44        73.55        49.25 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       13.97        32.84        16.57         4.41         4.77         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0996 TCGA-20-1684 
        3.91         3.09         8.42        23.05        72.20        19.10 
TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 TCGA-23-1032 TCGA-23-1111 TCGA-23-1113 
       47.54        15.39        26.83         2.24         3.22        31.20 
TCGA-23-1118 TCGA-23-1123 TCGA-23-2072 TCGA-23-2081 TCGA-23-2084 TCGA-23-2645 
       86.01        33.47        24.95        77.00        49.84         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        7.63        11.64        21.80        41.56         7.66        54.12 
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-24-1426 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 
        5.36         4.83        18.67         8.55        72.92        45.14 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
      105.99         1.18        26.96        57.40        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 
       56.58        41.06        41.39        39.88        44.09        45.50 
TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       10.26        17.23        90.15        48.33        38.24         8.32 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 
        3.72         4.37         5.79         5.52        22.68        30.21 
TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 
       11.05        81.11         4.87        44.84        58.16       109.71 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 
       14.43        28.18        44.52         0.36        31.63        70.45 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1315 
       67.36        36.23        33.11        55.86        53.26        51.06 
TCGA-25-1316 TCGA-25-1320 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 
       37.02        36.95         2.96        18.58        18.02        15.81 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-2042 
       20.61         0.30        56.94        60.59        51.22        13.02 
TCGA-25-2391 TCGA-25-2396 TCGA-25-2399 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       49.05         3.02        19.99        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 
       44.71       101.79        38.53        33.70        31.20         0.53 
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        17.00        85.68 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       39.12        12.36        11.84         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       34.62        62.47        45.11        42.25        11.47         9.76 
TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        0.26        44.91        34.78         6.12        36.62         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-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       44.12        28.77        29.10        22.55         8.55        25.74 
TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 
       29.82        25.91        25.08        23.80        20.98        14.17 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        6.05        16.18         7.99        42.02         7.46        40.77 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       11.38        21.14        29.00       180.20        80.12        22.32 
TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
       34.39         5.42        11.11        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1736 TCGA-61-1738 TCGA-61-1901 TCGA-61-1903 
       27.88        31.79        48.79        35.80        11.41        13.02 
TCGA-61-1911 TCGA-61-1995 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       42.51         2.01        17.98         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2109 
        4.80        51.72        61.64        58.39        55.50        20.68 
TCGA-61-2110 TCGA-OY-A56P TCGA-VG-A8LO 
       44.52        39.68         0.79 

  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                         0.36                          0.26 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                       152.02                        180.20 
  AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE 
                        26.04                         29.82 
[1] "0.4 - 152.0 (26.0)" "0.3 - 180.2 (29.8)"
[1] "hr=" "1.2"
D10V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 10(6P22.3) MUTATED         1   291                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                                    1                             1
  OVARY                                    291                           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, continuous
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED     2 296
  AMP PEAK 10(6P22.3) WILD-TYPE   1 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      2  296
  AMP PEAK 10(6P22.3) WILD-TYPE    1  272
     clus
vv    AMP PEAK 10(6P22.3) MUTATED AMP PEAK 10(6P22.3) WILD-TYPE
  NO                            2                             1
  YES                         296                           272
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 10(6P22.3) MUTATED    8 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                           8                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(6P22.3) MUTATED                                  2     7
  AMP PEAK 10(6P22.3) WILD-TYPE                                1    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(6P22.3) MUTATED                          15
  AMP PEAK 10(6P22.3) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(6P22.3) MUTATED                                           1   252
  AMP PEAK 10(6P22.3) WILD-TYPE                                         0   223
D10V7, multiclass
                                           clus
vv                                          AMP PEAK 10(6P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             252
                                           clus
vv                                          AMP PEAK 10(6P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               223
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(6P22.3) MUTATED     4 184
  AMP PEAK 10(6P22.3) WILD-TYPE   6 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(6P22.3) MUTATED      4  184
  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                         184
                        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   163 143
  AMP PEAK 11(7Q36.3) WILD-TYPE 103 147
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          306                           250 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                          143                           147 
$`AMP PEAK 11(7Q36.3) MUTATED`
TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
        2.01        46.62        18.51        63.09        21.57        65.46 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        33.67        71.47        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 
       41.59        19.99        29.10        84.20        48.89        27.88 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 
       64.64        36.23        31.86        45.37         9.47        17.98 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       38.43        89.33        41.62        57.60        61.87        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 
       17.98         5.85         3.02         8.55         6.18        35.15 
TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0926 
      112.41        63.09        39.75        20.94        26.93        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-13-0717 TCGA-13-0724 
       81.47        18.51        33.24        32.28        24.59         2.73 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 
       55.17        11.18        11.38        32.25        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 
       38.93        36.72        19.59         8.71         8.28        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       35.28        13.61        68.94        91.40        66.67        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 
       67.99        69.01        43.36        56.15        19.36        47.38 
TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       48.33        44.84        34.06        13.81         6.41         6.08 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
        6.61         6.05         4.70         4.21         5.33        87.06 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 
       29.42        98.04        20.68        82.88        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 
       49.25         4.24        54.31        38.40        32.84         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 
        4.41         4.77         4.18         2.56        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         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 
       42.54        26.83        31.76        18.90         2.24         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-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 
       41.56        54.12        63.55         6.31         7.82         7.99 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        6.02         5.95         5.36        28.37        19.17        18.67 
TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
        8.55        12.46        45.14         1.18        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1842 
       64.27        16.21        39.88        19.53        48.33         8.32 
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-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2033 
       30.21        11.05        81.11         4.87       152.02        18.48 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 
       44.52        57.07         0.79         0.36        47.54        70.45 
TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
        0.82        36.23        53.26         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       51.06         1.02        34.98        33.96         2.99        12.00 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1870 TCGA-25-1871 
       18.58        15.81         0.36        20.61        14.96        24.99 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 
       85.05        38.04         3.02        45.01        42.02         2.96 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 
       47.18         0.79        31.20        68.32         0.53        18.25 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 
       41.98        34.62        17.00        66.81        62.93        22.98 
TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       24.36        12.36        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 
        5.36        86.17        65.00        45.11         4.90        11.84 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1860 
       11.47        21.04        51.91        36.26         0.26        44.91 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1891 TCGA-31-1944 
       34.78         6.12        36.62         1.22        30.05        45.57 
TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-36-1568 TCGA-36-1577 TCGA-36-2529 
       18.77         6.71        42.51        28.77        25.74        35.05 
TCGA-36-2537 TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       25.91        21.60         2.24        18.31        20.52        14.17 
TCGA-36-2549 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
        6.05        11.47        26.04        23.74        42.02         7.46 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1586 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 
       40.77        24.03        22.32        25.08       180.20        80.12 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1725 
      116.12         9.40         2.14        44.81        20.52        31.43 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1743 TCGA-61-1895 
       27.88         4.34        31.79        44.84        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-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       37.05        42.51        48.92        56.61        67.76        15.75 
TCGA-61-1998 TCGA-61-2003 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 
        5.52         4.01        45.40         4.80         4.77        71.74 
TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 
       60.62        55.50         6.48        76.87        20.68        44.52 
TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22         8.61        39.68        18.94         0.79         8.05 

$`AMP PEAK 11(7Q36.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1343 TCGA-04-1346 
       40.24        41.00         1.81        49.15        11.87        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1525 TCGA-04-1530 
       48.76        63.98        49.28        76.57        38.37       119.08 
TCGA-04-1638 TCGA-04-1648 TCGA-04-1654 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 
       55.43        28.64        47.70        29.16        57.76        35.57 
TCGA-09-1659 TCGA-09-1664 TCGA-09-1668 TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 
        9.99        74.93        55.36        97.55         6.12         4.54 
TCGA-09-2050 TCGA-09-2056 TCGA-10-0925 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       71.11        12.46        54.31        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
       35.80        15.12        19.86         6.21        44.55        39.58 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0760 
       12.39        31.10        15.19        17.82         2.50        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0793 TCGA-13-0794 TCGA-13-0799 TCGA-13-0800 
       34.06        31.04        28.70        30.35         7.79         8.12 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0884 TCGA-13-0886 TCGA-13-0889 TCGA-13-0897 
        8.19        35.28       107.18        74.27        61.84        57.47 
TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 
       57.07        47.84        44.94        37.08        27.72        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-1403 TCGA-13-1405 TCGA-13-1408 
       21.17        14.89         4.64        10.88         7.36         5.92 
TCGA-13-1409 TCGA-13-1477 TCGA-13-1482 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
        6.84        54.64        61.71        22.39        70.82        52.44 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1511 TCGA-13-1512 TCGA-20-0990 
       37.61        13.97        16.57         3.91         3.09        25.94 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       72.20        25.38        19.10        47.54        40.54        15.39 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1116 
       49.41         8.81        29.13        51.35        54.51         4.57 
TCGA-23-1117 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-24-0970 TCGA-24-0975 
       33.30        39.09        33.47         0.53        11.64        21.80 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1105 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 
        7.66        22.32        47.41         6.38         7.86         0.76 
TCGA-24-1423 TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 
        6.25         4.83        17.39        43.53        72.92       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1545 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
        9.11         3.45        57.40        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 TCGA-24-1562 
       41.39        58.09        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-24-1616 TCGA-24-1843 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2023 
       38.24         3.48         5.79        22.68        16.44        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        53.95        28.18 
TCGA-24-2036 TCGA-24-2260 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2293 
       64.01        36.16        31.63        44.61        67.36        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1329 
       33.11        55.86        37.02        65.00        36.95         2.96 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       18.02         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 
       51.22        18.05        13.02        49.05         1.02        12.00 
TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       19.99        29.03        31.00        26.99        78.90        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
      101.79        38.53        33.70        16.90        18.67        59.67 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 
       29.23        85.68        39.12        31.23        22.55        17.33 
TCGA-29-1776 TCGA-29-1785 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 TCGA-30-1714 
       11.84        34.62        62.47        42.25         9.76        38.07 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 
        2.47        15.68        48.10        57.57        24.26        48.79 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 
       30.18        22.49        44.12         2.20        29.10        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        30.08        27.85        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-36-2544 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2593 TCGA-57-1583 
       20.98        16.18         7.99         9.44         1.48        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2350 TCGA-59-2354 
       21.14         1.74        29.00        25.02        22.32        34.39 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1734 
        5.42        11.11         8.09        20.94        18.54        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1907 TCGA-61-1917 
       48.79        35.80         2.43        33.67        31.30        43.43 
TCGA-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
       38.17         2.01        14.50        17.98        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 
       30.64         1.18        45.96        51.72        61.64        58.39 
TCGA-61-2098 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 
       65.52       125.75         6.35        31.07 

  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                        125.75 
  AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE 
                        24.97                         30.13 
[1] "0.3 - 180.2 (25.0)" "0.3 - 125.8 (30.1)"
[1] "hr=" "1.2"
D11V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 11(7Q36.3) MUTATED         1   308                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                                    1                             1
  OVARY                                    308                           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, continuous
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q36.3) MUTATED     1 313
  AMP PEAK 11(7Q36.3) WILD-TYPE   2 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q36.3) MUTATED      1  313
  AMP PEAK 11(7Q36.3) WILD-TYPE    2  255
     clus
vv    AMP PEAK 11(7Q36.3) MUTATED AMP PEAK 11(7Q36.3) WILD-TYPE
  NO                            1                             2
  YES                         313                           255
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 11(7Q36.3) MUTATED   10 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                          10                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(7Q36.3) MUTATED                                  0     7
  AMP PEAK 11(7Q36.3) WILD-TYPE                                3    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(7Q36.3) MUTATED                          21
  AMP PEAK 11(7Q36.3) WILD-TYPE                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(7Q36.3) MUTATED                                           1   261
  AMP PEAK 11(7Q36.3) WILD-TYPE                                         0   214
D11V7, multiclass
                                           clus
vv                                          AMP PEAK 11(7Q36.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             261
                                           clus
vv                                          AMP PEAK 11(7Q36.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               214
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q36.3) MUTATED     4 184
  AMP PEAK 11(7Q36.3) WILD-TYPE   6 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q36.3) MUTATED      4  184
  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                         184
                        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    88 113
  AMP PEAK 12(8P11.21) WILD-TYPE 178 177
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           201                            355 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           113                            177 
$`AMP PEAK 12(8P11.21) MUTATED`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1356 
       41.00        18.51        11.87        63.09        21.57        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       44.32        33.67        71.47        84.20        55.43        27.88 
TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1667 TCGA-09-1668 
       31.86        29.16         9.47        35.57        61.87        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-2043 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
       17.98         5.85         6.18       112.41        63.09        39.75 
TCGA-09-2054 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 
       20.94        33.24        35.44        35.80        24.59        39.58 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 
       31.10        17.82        55.17        34.06        31.04         8.45 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
       36.72        30.35         8.12         8.19        43.86        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0893 TCGA-13-0899 
       13.61        68.94       107.18        91.40        43.36        56.15 
TCGA-13-0901 TCGA-13-0908 TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 TCGA-13-1408 
       19.36        44.84        27.72        14.89        13.81         5.92 
TCGA-13-1409 TCGA-13-1481 TCGA-13-1485 TCGA-13-1489 TCGA-13-1497 TCGA-13-1504 
        6.84        87.06        20.68        82.88        54.31        16.57 
TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0991 
        4.41         3.91        14.24        10.78         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         4.57 
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-24-0968 TCGA-24-0979 TCGA-24-1418 
      115.89        49.84         4.50        19.66        41.56         7.99 
TCGA-24-1423 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 
        6.25         4.83        18.67         8.55        12.46        45.14 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 
      105.99         3.45         1.18        22.22        26.96        64.27 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1564 
       41.39        58.09        70.62        39.88        19.53        25.87 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 
       17.23        88.37        48.33         3.72         3.81        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-2019 TCGA-24-2023 
        5.79         5.52        22.68        30.21         4.87        44.84 
TCGA-24-2030 TCGA-24-2260 TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
       53.95        36.16        47.54         0.82        67.36        33.11 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1329 TCGA-25-1623 
        1.02        34.98        36.95        33.96         2.96        18.58 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1632 TCGA-25-1633 TCGA-25-1871 TCGA-25-1877 
        0.36        20.61        56.94        60.59        24.99        18.05 
TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-29-1691 TCGA-29-1693 
       85.05         1.02        38.04        45.01        47.18       101.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1761 TCGA-29-1763 
       31.20        68.32        16.90        18.67        17.00        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-2414 
       62.93        39.12        12.36        12.30        14.93        86.17 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 
       45.11        42.25        11.84        11.47        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1859 TCGA-30-1861 TCGA-30-1892 TCGA-31-1951 
       36.26         2.47        48.10        34.78        48.79        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-36-1570 TCGA-36-1576 TCGA-36-1581 TCGA-36-2529 
        6.71        42.51        21.53        30.08        24.69        35.05 
TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 
        2.24        14.17        16.18        26.04         9.44         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2352 
       24.03        11.38         1.74        22.32        25.02         9.40 
TCGA-59-2355 TCGA-59-2372 TCGA-61-1722 TCGA-61-1727 TCGA-61-1728 TCGA-61-1740 
        2.14        44.81         8.09        18.54        27.88         2.43 
TCGA-61-1743 TCGA-61-1899 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1914 
       43.69         8.42        34.13        31.30        42.51        56.61 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 
       39.85        30.64         4.77         6.48       125.75         6.35 
TCGA-61-2614 TCGA-OY-A56Q TCGA-WR-A838 
        8.61        18.94         8.05 

$`AMP PEAK 12(8P11.21) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 
       40.24         1.81        49.15         2.01        46.62        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1365 TCGA-04-1371 
       48.76        63.98        65.46        32.52        76.57        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        41.59        19.99        38.37       119.08        29.10 
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-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       57.76        17.98         9.99        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       41.62        57.60        30.51         3.02         8.55        97.55 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 
        6.12        35.15         4.54        71.11        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 
       54.31        25.91        81.47        18.51        32.28        11.70 
TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 
        3.91        15.12        19.86         6.21        44.55         2.73 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       12.39        15.19         2.50        11.18        11.38        11.54 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       32.25        21.40        38.93        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
        7.79         8.28        35.28        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 
       61.84        67.99        69.01        57.47        57.07        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
       48.33        47.84        44.94        37.08        34.06        29.98 
TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       21.17         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        7.36         6.05         4.70         4.21         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 
       61.71        29.42        98.04        22.39        70.82        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       73.55        38.20        49.25         4.24        37.61        38.40 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       13.97        32.84         4.21         4.77         4.18         2.56 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.09        12.23         8.61         8.75         6.28        54.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
       23.05        25.94        72.20        27.52        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        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 
       26.83        31.76        49.41         8.81        29.13         2.24 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
       31.20        68.68        33.30       129.96         4.27        39.09 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-24-0966 
       87.48        91.66        77.00         2.76         4.70         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80         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-24-1424 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        19.17 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
       43.53        72.92         9.11        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.06        51.91        88.50        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1846 
       10.26        90.15        38.24         8.32         3.48         4.37 
TCGA-24-1920 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2024 
        9.80        16.44        11.05        81.11       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-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 
       44.52        57.07         0.79         0.36        31.63        70.45 
TCGA-24-2281 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       44.61        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-25-1322 
       26.96        32.02        51.06        37.02        65.00         2.99 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 
       12.00        18.02        15.81         7.86         0.30        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 
       51.22        14.96        13.02        49.05         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1699 
       78.90        44.71        38.53         0.79        33.70         0.53 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       59.67        18.25        41.98        29.23        34.62        85.68 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       31.23        22.98        24.36        22.55        17.33        11.84 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23         5.36        34.62        65.00        62.47 
TCGA-29-2429 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
        4.90         9.76        21.04        15.68         0.26        44.91 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
        6.12        36.62         1.22        57.57        24.26        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 
       45.57        30.18        18.77        44.12         2.20        28.77 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 
       29.10        22.85        22.55         8.55        25.74        27.85 
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-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 
       23.80        21.60        20.98        18.31        20.52         6.05 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       11.47         7.99        23.74        42.02         7.46        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-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
      116.12        34.39         5.42        20.52        11.11        20.94 
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-61-1741 TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       35.80        33.67         1.45         5.79        11.41        13.02 
TCGA-61-1904 TCGA-61-1910 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
        9.07        37.05        48.92        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-61-2016 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-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       71.74        61.64        58.39        60.62        65.52        55.50 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P 
       76.87        20.68        44.52        22.22        31.07        39.68 
TCGA-VG-A8LO 
        0.79 

  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                          0.36                           0.26 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                        125.75                         180.20 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                         26.96                          28.64 
[1] "0.4 - 125.8 (27.0)" "0.3 - 180.2 (28.6)"
[1] "hr=" "1.2"
D12V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 12(8P11.21) MUTATED         0   201                2
  AMP PEAK 12(8P11.21) WILD-TYPE       2   356                0
D12V3, multiclass
                  clus
vv                 AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     201                            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, continuous
D12V5, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED     2 207
  AMP PEAK 12(8P11.21) WILD-TYPE   1 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      2  207
  AMP PEAK 12(8P11.21) WILD-TYPE    1  361
     clus
vv    AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  NO                             2                              1
  YES                          207                            361
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 12(8P11.21) MUTATED    4 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                            4                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(8P11.21) MUTATED                                  1     6
  AMP PEAK 12(8P11.21) WILD-TYPE                                2    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(8P11.21) MUTATED                          12
  AMP PEAK 12(8P11.21) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 12(8P11.21) MUTATED                                           0
  AMP PEAK 12(8P11.21) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 12(8P11.21) MUTATED     175
  AMP PEAK 12(8P11.21) WILD-TYPE   300
D12V7, multiclass
                                           clus
vv                                          AMP PEAK 12(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              175
                                           clus
vv                                          AMP PEAK 12(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                300
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED     3 115
  AMP PEAK 12(8P11.21) WILD-TYPE   7 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      3  115
  AMP PEAK 12(8P11.21) WILD-TYPE    7  210
                        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                            210
[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   214 227
  AMP PEAK 13(8Q24.21) WILD-TYPE  52  63
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           441                            115 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           227                             63 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       65.52        21.57        65.46        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       33.67        76.57        41.59        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       29.10        84.20        27.88        36.23        31.86        47.70 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       29.16         9.47        17.98         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-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 
       35.15       112.41        71.11        63.09        26.93        12.46 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       54.31        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
        3.91        35.44        35.80        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       24.59        44.55        39.58         2.73        12.39        31.10 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       55.17         2.50        11.38        11.54        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       30.35         8.71         8.12         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       35.28        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       66.67        67.99        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 
       19.36        47.38        48.33        47.84        44.94        44.84 
TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 
       27.72        29.98        21.17        14.89        13.81         4.64 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1408 TCGA-13-1410 
        6.41         6.08        10.88         6.61         5.92         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.21         5.33        87.06        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       20.68        70.82        38.20         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 
        4.77         4.18         2.56         3.91         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         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-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       16.70         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 
       18.90        51.35        54.51         3.22         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
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-24-0975 TCGA-24-0979 
       49.84         2.76         4.70         4.50        21.80        41.56 
TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
        7.66        22.32        54.12        63.55        47.41         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.25         5.95 
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-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       12.46        45.14       105.99         3.45         1.18        22.22 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 
       57.40        64.27        56.58        41.06        41.39        58.09 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 
       88.50        70.62        39.88        19.53        47.70        25.87 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        88.37        48.33         8.32         3.72 
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-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        11.05         4.87       152.02        44.84 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
       53.95        18.48        28.18        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-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 
       53.26         1.02        26.96        32.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       65.00        36.95        33.96         2.99         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 
       18.02        15.81         0.36        20.61         7.86        56.94 
TCGA-25-1635 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2396 
       51.22        18.05        85.05        13.02         1.02         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-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        44.71       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.70        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 
       59.67        18.25        29.23        34.62        17.00        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 
       62.93        39.12        31.23        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-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        11.84         9.76        21.04        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 
       36.26         2.47        15.68         0.26        48.10        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
        6.12        36.62        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-36-1574 
        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-36-2534 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-36-2548 TCGA-36-2549 
        2.24        20.98        18.31        20.52        14.17         6.05 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        7.99        26.04         9.44        42.02         7.46        40.77 
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-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 
       25.02       180.20       116.12         9.40        34.39         2.14 
TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        44.81        20.52        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-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1904 
       33.67        43.69         8.42         5.79        11.41         9.07 
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-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        15.75        38.17         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2088 
       17.98         4.01        30.64        39.85         1.18         4.77 
TCGA-61-2092 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       51.72        58.39        60.62        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       20.68        22.22         6.35        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

$`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 
       40.24         2.01        63.09        48.76        63.98        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       82.39        56.55        55.43        48.89        28.64        64.64 
TCGA-04-1655 TCGA-09-0366 TCGA-09-0369 TCGA-09-1664 TCGA-09-2048 TCGA-09-2053 
       45.37        57.76        35.57        74.93         4.54        39.75 
TCGA-09-2054 TCGA-10-0926 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0795 
       20.94        25.91        15.19        17.82        11.18        19.59 
TCGA-13-0799 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0910 
        7.79        74.27        70.39        61.84        69.01        37.08 
TCGA-13-0912 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1487 
       34.06         7.36         6.05         6.84        54.64        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-2057 TCGA-20-0996 
       82.88        52.44        73.55        49.25        14.24        72.20 
TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 TCGA-23-1809 TCGA-24-0966 TCGA-24-0968 
        2.24        31.20        68.68         0.53         7.63        19.66 
TCGA-24-0970 TCGA-24-1413 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 
       11.64         6.31         6.02         5.36        28.37        19.17 
TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 TCGA-24-1551 TCGA-24-1560 TCGA-24-1562 
        9.11        26.96        16.21        51.91        44.09        45.50 
TCGA-24-1565 TCGA-24-1616 TCGA-24-1843 TCGA-24-1850 TCGA-24-1930 TCGA-24-2024 
       10.26        38.24         3.48         5.52        81.11        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2038 TCGA-25-1315 TCGA-25-1316 
       34.82       109.71        14.43        44.52        51.06        37.02 
TCGA-25-1323 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
       12.00         0.30        60.59        35.54        14.96        24.99 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2408 TCGA-29-1691 TCGA-29-1707 TCGA-29-1762 
       49.05        38.04        31.00        47.18        41.98        85.68 
TCGA-29-1771 TCGA-29-1774 TCGA-29-2434 TCGA-30-1860 TCGA-30-1867 TCGA-30-1880 
       22.55        17.33        11.47        44.91         1.22        57.57 
TCGA-36-2532 TCGA-36-2540 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2593 
       29.49        23.80        16.18        11.47        23.74         1.48 
TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-61-1721 TCGA-61-1722 TCGA-61-1730 
       29.00        80.12        22.32        11.11         8.09         4.34 
TCGA-61-1733 TCGA-61-1895 TCGA-61-1903 TCGA-61-1995 TCGA-61-2012 TCGA-61-2017 
       31.79         1.45        13.02         2.01        30.64        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2110 
       45.40         4.80        71.74        61.64        65.52        44.52 
TCGA-61-2111 
      125.75 

  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                         125.75 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         26.96                          31.20 
[1] "0.3 - 180.2 (27.0)" "0.3 - 125.8 (31.2)"
[1] "hr=" "1.1"
D13V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 13(8Q24.21) MUTATED         2   441                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                                     2                              0
  OVARY                                     441                            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, continuous
D13V5, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     2 451
  AMP PEAK 13(8Q24.21) WILD-TYPE   1 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      2  451
  AMP PEAK 13(8Q24.21) WILD-TYPE    1  117
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                             2                              1
  YES                          451                            117
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 13(8Q24.21) MUTATED   11 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                           11                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(8Q24.21) MUTATED                                  2    16
  AMP PEAK 13(8Q24.21) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(8Q24.21) MUTATED                          26
  AMP PEAK 13(8Q24.21) WILD-TYPE                         6
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 13(8Q24.21) MUTATED                                           1
  AMP PEAK 13(8Q24.21) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 13(8Q24.21) MUTATED     375
  AMP PEAK 13(8Q24.21) WILD-TYPE   100
D13V7, multiclass
                                           clus
vv                                          AMP PEAK 13(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                           26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              375
                                           clus
vv                                          AMP PEAK 13(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                  2
  BLACK OR AFRICAN AMERICAN                                              6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                100
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     7 260
  AMP PEAK 13(8Q24.21) WILD-TYPE   3  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      7  260
  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                          260
                        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   110 137
  AMP PEAK 14(10P15.3) WILD-TYPE 156 153
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           247                            309 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                           137                            153 
$`AMP PEAK 14(10P15.3) MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
       41.00        46.62        11.87        65.52        63.09        48.76 
TCGA-04-1349 TCGA-04-1356 TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 
       21.57        49.28        19.99       119.08        84.20        27.88 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0367 
       64.64        31.86        47.70        45.37         9.47        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 
       35.57         9.99        38.43        41.62        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 
       30.51        17.98         5.85         3.02         8.55         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 
       35.15       112.41        71.11        33.24        11.70        35.44 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       39.58         2.73        31.10        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
       11.18        11.54        31.04         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       30.35         8.12         8.19        13.61       107.18        91.40 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0904 
       66.67        70.39        69.01        43.36        57.07        48.33 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       27.72        14.89        13.81         6.05         6.84         4.70 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       54.64        87.06        98.04        70.82        82.88        52.44 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1509 TCGA-13-1512 
       49.25         4.24        54.31        37.61         4.18         3.09 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-20-0987 TCGA-20-1683 
       12.23         8.61        10.78         6.28        23.05        25.38 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1028 
       16.70         2.93        47.54        42.54        15.39        49.41 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1110 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 
        8.81        18.90        54.51        33.30        86.01         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-24-0970 TCGA-24-0982 
       39.09        33.47        58.13       115.89        11.64        22.32 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
       47.41         7.82         7.99         6.02         4.83        17.39 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 TCGA-24-1544 TCGA-24-1548 
       18.67         8.55        45.14         9.11        26.96        16.21 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 
       70.62        39.88        25.87        10.26        88.37        48.33 
TCGA-24-1616 TCGA-24-1843 TCGA-24-1924 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 
       38.24         3.48        30.21        11.05       152.02        44.84 
TCGA-24-2030 TCGA-24-2260 TCGA-24-2261 TCGA-24-2288 TCGA-24-2289 TCGA-24-2295 
       53.95        36.16         0.79         0.82        67.36        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 
       55.86        53.26         1.02         1.02        36.95        33.96 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
        2.96        18.58        15.81         0.36        20.61         0.30 
TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 
       35.54        24.99        18.05        85.05        49.05         1.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-29-1691 TCGA-29-1695 TCGA-29-1701 
       12.00        45.01         2.96        47.18         0.79        16.90 
TCGA-29-1702 TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 
       18.67        41.98        29.23        66.81        39.12        22.98 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       17.33        12.36        12.30        14.93         8.38         7.23 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 
       34.62        86.17        65.00        45.11         4.90        11.84 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
       11.47         9.76        21.04        51.91        36.26        15.68 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-31-1944 
       44.91        34.78        36.62         1.22        24.26        45.57 
TCGA-31-1950 TCGA-31-1953 TCGA-36-1569 TCGA-36-1571 TCGA-36-1577 TCGA-36-1578 
       18.77         6.71        29.10        22.85        25.74        27.85 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2542 
       24.23        24.69        35.05        33.01        29.49        21.60 
TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 
        2.24        14.17         6.05        16.18        11.47        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 
        9.44        42.02         1.48        24.03        11.38        22.32 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2352 TCGA-59-2372 TCGA-59-A5PD 
       25.08        25.02       180.20         9.40        44.81        20.52 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
        8.09        20.94        27.88         4.34        31.79        28.47 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 TCGA-61-1917 
        2.43        33.67         9.07        34.13        42.51        43.43 
TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 
       15.75        38.17         4.01        30.64        45.40         4.77 
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-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22         6.35        31.07        39.68        18.94         0.79 
TCGA-WR-A838 
        8.05 

$`AMP PEAK 14(10P15.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1350 
       40.24         1.81        49.15         2.01        18.51        63.98 
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        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 
       82.39        56.55        41.59        38.37        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-09-0364 TCGA-09-0366 TCGA-09-1662 
       48.89        28.64        36.23        29.16        57.76        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1675 TCGA-09-2043 TCGA-09-2048 TCGA-09-2051 
       74.93        57.60        97.55         6.18         4.54        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       81.47        18.51        32.28         3.91        35.80        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0755 
       19.86         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        34.06        32.25        21.40        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        8.71         7.79         8.28        43.86        35.28        35.28 
TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 TCGA-13-0899 
       68.94        74.27        61.84        67.99        57.47        56.15 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        47.84        44.94        44.84        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 
       10.88         6.61         7.36         5.92         4.21         5.33 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1492 TCGA-13-1494 
       61.71        29.42        20.68        22.39        73.55        38.20 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       38.40        13.97        32.84        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2065 TCGA-13-A5FT 
        4.77         2.56         3.91        14.24         8.75        54.77 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 
        8.42        25.94        26.20        72.20        27.52        19.10 
TCGA-20-1687 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1030 TCGA-23-1032 
        2.66        40.54        26.83        31.76        29.13         2.24 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1119 
       51.35         3.22        31.20        68.68         4.57       129.96 
TCGA-23-1120 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
        4.27         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-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
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        19.17        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        32.02        51.06 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1625 
       37.02        34.98        65.00         2.99        12.00        18.02 
TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 
        7.86        56.94        60.59        51.22        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        44.71       101.79        38.53        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 
       31.20        68.32         0.53        59.67        18.25        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 
       17.00        85.68        62.93        31.23        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-3P-A9WA 
       25.08        23.80        20.98        18.31        20.52         7.99 
TCGA-42-2582 TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 
       26.04         7.46        40.77        21.14         1.74        29.00 
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-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       11.11        31.43        18.54        48.79        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-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1995 
       31.30        37.05        48.92        56.61        67.76         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-61-2087 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-61-2104 TCGA-61-2614 
       60.62        76.87         8.61 

  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                         129.96 
  AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE 
                         25.38                          29.10 
[1] "0.3 - 180.2 (25.4)" "0.3 - 130.0 (29.1)"
[1] "hr=" "1.2"
D14V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 14(10P15.3) MUTATED         0   246                2
  AMP PEAK 14(10P15.3) WILD-TYPE       2   311                0
D14V3, multiclass
                  clus
vv                 AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     246                            311
  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, continuous
D14V5, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.3) MUTATED     2 248
  AMP PEAK 14(10P15.3) WILD-TYPE   1 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.3) MUTATED      2  248
  AMP PEAK 14(10P15.3) WILD-TYPE    1  320
     clus
vv    AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE
  NO                             2                              1
  YES                          248                            320
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(10P15.3) MUTATED    8 16  4  1
  AMP PEAK 14(10P15.3) WILD-TYPE  6 10  1  2
D14V6, multiclass
    clus
vv   AMP PEAK 14(10P15.3) MUTATED AMP PEAK 14(10P15.3) WILD-TYPE
  R0                            8                              6
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(10P15.3) MUTATED                                  1     9
  AMP PEAK 14(10P15.3) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(10P15.3) MUTATED                           9
  AMP PEAK 14(10P15.3) WILD-TYPE                        23
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 14(10P15.3) MUTATED                                           1
  AMP PEAK 14(10P15.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 14(10P15.3) MUTATED     216
  AMP PEAK 14(10P15.3) WILD-TYPE   259
D14V7, multiclass
                                           clus
vv                                          AMP PEAK 14(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              216
                                           clus
vv                                          AMP PEAK 14(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                259
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.3) MUTATED     7 149
  AMP PEAK 14(10P15.3) WILD-TYPE   3 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.3) MUTATED      7  149
  AMP PEAK 14(10P15.3) WILD-TYPE    3  176
                        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                            176
[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    91  87
  AMP PEAK 15(10Q22.3) WILD-TYPE 175 203
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                           178                            378 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                            87                            203 
$`AMP PEAK 15(10Q22.3) MUTATED`
TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       46.62        18.51        63.09        21.57        63.98        49.28 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1517 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 
       44.32        76.57        19.99       119.08        84.20        27.88 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 TCGA-09-1666 
       31.86        45.37         9.47         9.99        38.43        57.60 
TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2044 TCGA-09-2048 
       61.87        17.98         5.85         8.55         6.12         4.54 
TCGA-09-2055 TCGA-10-0928 TCGA-10-0930 TCGA-13-0714 TCGA-13-0720 TCGA-13-0727 
       26.93        18.51        33.24         6.21        44.55        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0762 TCGA-13-0791 TCGA-13-0792 
       17.82        55.17        11.18        32.25        38.93        36.72 
TCGA-13-0802 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 
        8.19       107.18        91.40        66.67        67.99        69.01 
TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 TCGA-13-0913 TCGA-13-0919 
       43.36        57.07        19.36        47.84        29.98        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-1405 TCGA-13-1477 TCGA-13-1484 TCGA-13-1495 
       13.81         6.41         7.36        54.64        98.04        49.25 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.24        16.57         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1682 TCGA-20-1685 TCGA-20-1687 
        3.09        54.77        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         2.24        54.51        33.30        86.01        33.47 
TCGA-23-2077 TCGA-23-2079 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0970 
      115.89        91.66         4.70         4.50        19.66        11.64 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
       22.32        63.55         6.25         6.02         4.83        17.39 
TCGA-24-1434 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 
       18.67        16.21        56.58        51.91        58.09        70.62 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1842 TCGA-24-1844 TCGA-24-1847 TCGA-24-1849 
       47.70        25.87         8.32         3.72        11.28         5.79 
TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2261 TCGA-24-2288 
       16.44        11.05        81.11         4.87         0.79         0.82 
TCGA-24-2293 TCGA-24-2297 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 
       16.64        55.86        32.02         1.02        34.98        33.96 
TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1877 TCGA-25-2042 
       12.00        18.58        15.81        35.54        18.05        13.02 
TCGA-25-2392 TCGA-25-2397 TCGA-25-2404 TCGA-29-1693 TCGA-29-1710 TCGA-29-1763 
        1.02        12.00        29.03       101.79        29.23        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1775 TCGA-29-1777 TCGA-29-1783 TCGA-29-2425 
       62.93        39.12        12.36        12.30         7.23        65.00 
TCGA-29-2428 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1860 
       45.11         9.76        21.04        36.26         2.47        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-36-1578 TCGA-36-1580 
       34.78        36.62         1.22        18.77        27.85        24.23 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 
       35.05        29.49        29.82         2.24        20.52        14.17 
TCGA-36-2552 TCGA-42-2588 TCGA-57-1583 TCGA-57-1585 TCGA-59-2348 TCGA-59-2351 
       11.47         9.44        11.38         1.74       180.20       116.12 
TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 
        5.42        44.81         8.09        20.94        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1901 TCGA-61-1904 
        4.34        31.79        48.79        44.84        11.41         9.07 
TCGA-61-1910 TCGA-61-1915 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
       37.05        67.76        14.50         4.01        30.64        30.64 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 
       58.39        65.52        55.50         6.48        20.68        44.52 
TCGA-61-2111 TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 
      125.75         6.35        18.94         8.05 

$`AMP PEAK 15(10Q22.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 
       40.24        41.00         1.81        49.15         2.01        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 
       65.52        48.76        65.46        32.52        33.67        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1536 TCGA-04-1638 
       82.39        56.55        41.59        38.37        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
       48.89        28.64        64.64        36.23        47.70        29.16 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       57.76        17.98        35.57        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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       54.31        25.91        81.47        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 
       35.44        35.80        15.12        19.86        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        31.10         2.50        11.38        11.54 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 TCGA-13-0794 
       34.06        31.04        21.40         8.45        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 
       19.59         8.71         7.79         8.12         8.28        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0888 
       35.28        35.28        13.61        68.94        74.27        70.39 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       61.84        57.47        56.15        47.38        48.33        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 
       44.84        37.08        27.72        34.06        21.17         4.64 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.08        10.88         6.61         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 
        4.70         4.21         5.33        87.06        61.71        29.42 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       20.68        22.39        70.82        82.88        52.44        73.55 
TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       38.20        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        4.21         4.41        14.24        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 
        8.75         6.28         8.42        23.05        26.20        72.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 
       25.38        19.10         2.93        42.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1119 
       51.35         3.22        31.20        68.68         4.57       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27         6.38        39.09        58.13         0.53        24.95 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0975 
       87.48        77.00        49.84         2.76         7.63        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       41.56         7.66        54.12        47.41         6.31         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 TCGA-24-1426 
        7.82         7.99         7.86         0.76         5.95         5.36 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
       28.37        19.17        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 
       45.14       105.99         9.11         3.45         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 
       26.96        57.40        64.27        41.06        41.39        88.50 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 
       39.88        19.53        44.09        45.50        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-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-2020 
        4.37         5.52         9.80        22.68        30.21       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        53.95 
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-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
        0.36        47.54        31.63        70.45        44.61        67.36 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1315 
       36.23        33.11        53.26         1.02        26.96        51.06 
TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 
       37.02        65.00        36.95         2.99         2.96        18.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2391 TCGA-25-2393 
       51.22        14.96        24.99        85.05        49.05        38.04 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 
        3.02        45.01        19.99        42.02         2.96        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 
       26.99        78.90        44.71        47.18        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.70        31.20        68.32         0.53        16.90        18.67 
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        17.00        85.68 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       31.23        22.98        24.36        22.55        17.33        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 
       14.93         8.38         5.36        34.62        86.17        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 
        4.90        42.25        11.84        11.47        38.07        51.91 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1880 TCGA-30-1887 
       15.68         0.26        48.10         6.12        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-36-1581 
       22.85        22.55         8.55        30.08        25.74        24.69 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 
       33.01        25.91        25.08        23.80        21.60        20.98 
TCGA-36-2545 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       18.31         6.05        16.18         7.99        26.04        23.74 
TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 
       42.02         7.46        40.77         1.48        24.03        21.14 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 
       22.32        29.00        25.08        25.02        80.12        22.32 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1725 
        9.40        34.39         2.14        20.52        11.11        31.43 
TCGA-61-1734 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 
       28.47        35.80         2.43        33.67        43.69         1.45 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 
        8.42         5.79        13.02        34.13        31.30        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        56.61        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        5.52        17.98        39.85         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 
        4.80         4.77        51.72        71.74        61.64        60.62 
TCGA-61-2104 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
       76.87        22.22        31.07         8.61        39.68         0.79 

  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                          0.79                           0.26 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                        180.20                         152.02 
  AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE 
                        23.275                         29.100 
[1] "0.8 - 180.2 (23.3)" "0.3 - 152.0 (29.1)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 15(10Q22.3) MUTATED         1   177                2
  AMP PEAK 15(10Q22.3) WILD-TYPE       1   380                0
D15V3, multiclass
                  clus
vv                 AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     177                            380
  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, continuous
D15V5, binary
                                cls
clus                               0   1
  AMP PEAK 15(10Q22.3) MUTATED     1 180
  AMP PEAK 15(10Q22.3) WILD-TYPE   2 388
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10Q22.3) MUTATED      1  180
  AMP PEAK 15(10Q22.3) WILD-TYPE    2  388
     clus
vv    AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE
  NO                             1                              2
  YES                          180                            388
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 15(10Q22.3) MUTATED    6  7  1  2
  AMP PEAK 15(10Q22.3) WILD-TYPE  8 19  4  1
D15V6, multiclass
    clus
vv   AMP PEAK 15(10Q22.3) MUTATED AMP PEAK 15(10Q22.3) WILD-TYPE
  R0                            6                              8
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(10Q22.3) MUTATED                                  2     8
  AMP PEAK 15(10Q22.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(10Q22.3) MUTATED                           8
  AMP PEAK 15(10Q22.3) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 15(10Q22.3) MUTATED                                           0
  AMP PEAK 15(10Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 15(10Q22.3) MUTATED     150
  AMP PEAK 15(10Q22.3) WILD-TYPE   325
D15V7, multiclass
                                           clus
vv                                          AMP PEAK 15(10Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              150
                                           clus
vv                                          AMP PEAK 15(10Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                 10
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                325
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(10Q22.3) MUTATED     3 104
  AMP PEAK 15(10Q22.3) WILD-TYPE   7 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(10Q22.3) MUTATED      3  104
  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                          104
                        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   120 125
  AMP PEAK 16(11Q14.1) WILD-TYPE 146 165
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           245                            311 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                           125                            165 
$`AMP PEAK 16(11Q14.1) MUTATED`
TCGA-04-1343 TCGA-04-1346 TCGA-04-1350 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       11.87        65.52        63.98        49.28        32.52        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1536 
       76.57        71.47        82.39        56.55        41.59        29.10 
TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-09-0366 
       84.20        48.89        27.88        64.64        31.86        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       17.98        35.57         9.99        38.43        89.33        41.62 
TCGA-09-1667 TCGA-09-1668 TCGA-09-1673 TCGA-09-2044 TCGA-09-2048 TCGA-09-2051 
       61.87        55.36         3.02         6.12         4.54        63.09 
TCGA-09-2055 TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0720 
       26.93        32.28        35.44        35.80         6.21        44.55 
TCGA-13-0723 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       39.58        31.10        55.17         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0791 TCGA-13-0792 TCGA-13-0802 TCGA-13-0885 TCGA-13-0887 
       32.25        38.93        36.72         8.19        91.40        66.67 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0904 
       67.99        69.01        43.36        57.47        56.15        48.33 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       47.84        44.84        14.89        13.81         4.64         6.41 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       10.88         6.61         6.05         5.92         4.70         4.21 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 TCGA-13-1497 
        5.33        87.06        29.42        22.39        82.88        54.31 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1506 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
       38.40        32.84         4.41        14.24        12.23         8.61 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 
        8.75         6.28         8.42        25.38        19.10        16.70 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1027 TCGA-23-1029 TCGA-23-1030 
        2.93        47.54        42.54        31.76         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 TCGA-23-1119 
       18.90         2.24        51.35         3.22         4.57       129.96 
TCGA-23-1120 TCGA-23-1124 TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2643 
        4.27        58.13        24.95        91.66        49.84         4.70 
TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
        4.50        19.66        21.80        54.12        63.55        47.41 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 TCGA-24-1428 
        7.82         7.99         0.76         6.25         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1469 
       19.17        18.67         8.55        72.92        45.14         9.11 
TCGA-24-1471 TCGA-24-1545 TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 
        1.18        57.40        56.58        51.91        58.09        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1563 TCGA-24-1564 TCGA-24-1604 TCGA-24-1616 
       39.88        19.53        47.70        25.87        88.37        38.24 
TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1920 
        8.32         3.72         3.81         4.37        11.28         9.80 
TCGA-24-1924 TCGA-24-1927 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 
       30.21        16.44        34.82       109.71        53.95        18.48 
TCGA-24-2035 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 
       28.18        57.07         0.36        47.54        44.61         0.82 
TCGA-24-2289 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1319 
       67.36        53.26         1.02        26.96        32.02        65.00 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1623 TCGA-25-1627 TCGA-25-1631 TCGA-25-1635 
       33.96         2.99        18.58         0.36         0.30        51.22 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2400 TCGA-29-1691 TCGA-29-1693 
       18.05        85.05         1.02        42.02        47.18       101.79 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 TCGA-29-1763 TCGA-29-1764 
        0.79        31.20        16.90        18.67        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 
       31.23        22.98        17.33        11.84        14.93         7.23 
TCGA-29-2425 TCGA-29-2429 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 
       65.00         4.90        11.47        21.04        51.91        36.26 
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-30-1891 TCGA-31-1946 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 
       36.62        30.05        30.18         2.20        28.77        21.53 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2534 
       22.55        30.08        27.85        24.23        33.01        29.82 
TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 
       20.52         6.05        16.18        11.47         7.99        23.74 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1994 TCGA-59-2348 
        1.48        11.38        21.14         1.74        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-61-1722 TCGA-61-1728 TCGA-61-1738 
      116.12         9.40         2.14         8.09        27.88        35.80 
TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 
        2.43        43.69         1.45        34.13        31.30        42.51 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2002 
       48.92        67.76        43.43        15.75        38.17        17.98 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2018 TCGA-61-2087 TCGA-61-2094 TCGA-61-2097 
       30.64        30.64        45.40         4.80        71.74        60.62 
TCGA-61-2098 TCGA-61-2104 TCGA-61-2109 TCGA-61-2612 TCGA-VG-A8LO 
       65.52        76.87        20.68         6.35         0.79 

$`AMP PEAK 16(11Q14.1) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 TCGA-04-1364 
       18.51        63.09        48.76        21.57        65.46        33.67 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1648 TCGA-04-1651 
       19.99        38.37       119.08        55.43        28.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-1664 TCGA-09-1666 
       47.70        45.37        29.16         9.47        74.93        57.60 
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-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 
       35.15       112.41        71.11        39.75        20.94        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 
       54.31        25.91        81.47        18.51        33.24        11.70 
TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0724 TCGA-13-0725 
        3.91        15.12        19.86        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        31.04        21.40 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
        8.45        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0900 
       68.94       107.18        74.27        70.39        61.84        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       19.36        47.38        44.94        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0924 TCGA-13-1405 TCGA-13-1409 TCGA-13-1477 
       29.98        21.17         6.08         7.36         6.84        54.64 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
       61.71        98.04        20.68        70.82        52.44        73.55 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 
       38.20        49.25         4.24        37.61        13.97        16.57 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.21         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2061 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       10.78        54.77        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        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 
       34.98        36.95        12.00         2.96        18.02        15.81 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 
       20.61         7.86        56.94        60.59        35.54        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        44.71        38.53        33.70        68.32         0.53 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        29.23        34.62        17.00 
TCGA-29-1762 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       85.68        39.12        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        34.62        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        11.84         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 
       26.04         9.44        42.02         7.46        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-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 
        5.42        44.81        20.52        11.11        20.94        31.43 
TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 
       18.54         4.34        31.79        28.47        48.79        44.84 
TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 
       33.67         8.42         5.79        11.41        13.02         9.07 
TCGA-61-1910 TCGA-61-1914 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       37.05        56.61         2.01         5.52        14.50         4.01 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 
       39.85         1.18        45.96         4.77        51.72        61.64 
TCGA-61-2096 TCGA-61-2101 TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       58.39        55.50         6.48        44.52       125.75        22.22 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       31.07         8.61        39.68        18.94         8.05 

  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                         152.02 
  AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE 
                         29.10                          26.99 
[1] "0.3 - 180.2 (29.1)" "0.5 - 152.0 (27.0)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 16(11Q14.1) MUTATED         0   249                0
  AMP PEAK 16(11Q14.1) WILD-TYPE       2   308                2
D16V3, multiclass
                  clus
vv                 AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     249                            308
  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, continuous
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q14.1) MUTATED     1 252
  AMP PEAK 16(11Q14.1) WILD-TYPE   2 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q14.1) MUTATED      1  252
  AMP PEAK 16(11Q14.1) WILD-TYPE    2  316
     clus
vv    AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
  NO                             1                              2
  YES                          252                            316
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 16(11Q14.1) MUTATED    5  9  3  1
  AMP PEAK 16(11Q14.1) WILD-TYPE  9 17  2  2
D16V6, multiclass
    clus
vv   AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
  R0                            5                              9
  R1                            9                             17
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(11Q14.1) MUTATED                                  1     7
  AMP PEAK 16(11Q14.1) WILD-TYPE                                2    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(11Q14.1) MUTATED                          15
  AMP PEAK 16(11Q14.1) WILD-TYPE                        17
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 16(11Q14.1) MUTATED                                           1
  AMP PEAK 16(11Q14.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 16(11Q14.1) MUTATED     211
  AMP PEAK 16(11Q14.1) WILD-TYPE   264
D16V7, multiclass
                                           clus
vv                                          AMP PEAK 16(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              211
                                           clus
vv                                          AMP PEAK 16(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                264
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(11Q14.1) MUTATED     3 141
  AMP PEAK 16(11Q14.1) WILD-TYPE   7 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(11Q14.1) MUTATED      3  141
  AMP PEAK 16(11Q14.1) WILD-TYPE    7  184
                        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                            184
[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   155 160
  AMP PEAK 17(12P13.33) WILD-TYPE 111 130
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            315                             241 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                            160                             130 
$`AMP PEAK 17(12P13.33) MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
       41.00        46.62        65.52        63.09        21.57        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 
       49.28        32.52        44.32        82.39        41.59        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1651 
       38.37       119.08        29.10        84.20        27.88        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       31.86        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 
       35.57         9.99        38.43        89.33        57.60        61.87 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 
       55.36        17.98         5.85         8.55         6.18         6.12 
TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 
        4.54        71.11        63.09        39.75        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0937 TCGA-10-0938 
       81.47        18.51        33.24        11.70        15.12        19.86 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
       24.59        39.58        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        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 
       21.40        36.72        30.35        19.59         8.71         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
        8.19        43.86        68.94        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 
       70.39        56.15        19.36        48.33        44.94        44.84 
TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-1407 TCGA-13-1411 
       34.06        21.17        13.81         6.41         6.05         4.21 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1495 TCGA-13-1496 
       98.04        20.68        22.39        82.88        49.25         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        32.84        16.57         4.21         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         2.56         3.91        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       10.78         8.75         6.28        54.77         8.42        25.94 
TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 
       27.52        16.70         2.93         2.66        47.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1031 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
       26.83        31.76        18.90         3.22        68.68         4.57 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       33.30       129.96         6.38        58.13         0.53       115.89 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1104 TCGA-24-1418 
        4.70         4.50        11.64        22.32        63.55         7.99 
TCGA-24-1424 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        6.02         4.83        28.37        19.17        18.67         8.55 
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-24-1548 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        64.27        16.21        51.91        41.39        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       70.62        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-24-1843 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-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 
       11.05        81.11         4.87       152.02        58.16        34.82 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 
       53.95        18.48        44.52        36.16        47.54        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-25-1318 TCGA-25-1321 
       53.26         1.02        26.96        32.02        34.98        33.96 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1634 
       12.00        18.02        15.81         0.36         7.86        35.54 
TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 
       51.22        24.99        18.05        85.05        13.02         1.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2409 TCGA-29-1690 
        3.02        12.00        45.01        42.02        26.99        44.71 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       47.18         0.79        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 
       18.67        59.67        29.23        17.00        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.12        31.23        22.98        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-29-2431 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 
       42.25        11.47        21.04        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-30-1880 TCGA-30-1887 TCGA-30-1891 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 
       57.57        24.26        30.05        18.77        42.51         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 
       29.10        22.85         8.55        30.08        25.74        27.85 
TCGA-36-1580 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 
       24.23        21.60        20.98        20.52        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 
       16.18        11.47         7.99        23.74         9.44        40.77 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 
        1.48        11.38        21.14        22.32        25.08        25.02 
TCGA-59-2348 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1722 
      180.20       116.12         9.40         5.42        44.81         8.09 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1738 TCGA-61-1741 
       27.88         4.34        31.79        28.47        35.80        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       43.69         1.45         8.42         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1919 
       34.13        31.30        48.92        67.76        43.43        38.17 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2097 
       17.98        39.85        30.64        45.40         4.77        60.62 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       76.87        44.52       125.75         6.35        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       39.68        18.94         8.05 

$`AMP PEAK 17(12P13.33) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 
       48.76        63.98        33.67        76.57        71.47        56.55 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 TCGA-09-1664 
       55.43        48.89        28.64        64.64        47.70        74.93 
TCGA-09-1665 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2049 
       41.62        30.51         3.02        97.55        35.15       112.41 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       20.94        26.93        54.31        32.28         3.91        35.44 
TCGA-10-0936 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 
       35.80         6.21        44.55         2.73        12.39        31.10 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 
        8.45        38.93        28.70         7.79         8.28        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       35.28        13.61       107.18        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0910 
       43.36        57.47        57.07        47.38        47.84        37.08 
TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 
       27.72        29.98        14.89         4.64         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        6.61         7.36         5.92         6.84         4.70         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1488 TCGA-13-1491 
       54.64        87.06        61.71        29.42        70.82        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1497 TCGA-13-1500 TCGA-13-1507 TCGA-13-1512 
       73.55        38.20        54.31        13.97         4.77         3.09 
TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-23-1022 
       23.05        26.20        72.20        25.38        19.10        42.54 
TCGA-23-1023 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
       40.54        49.41         8.81        29.13         2.24        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       54.51        31.20        86.01         4.27        39.09        33.47 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95        87.48        91.66        77.00        49.84         2.76 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        7.63        19.66        21.80        41.56         7.66        54.12 
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-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 
        6.25         5.95         5.36        17.39        43.53        72.92 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1549 TCGA-24-1550 TCGA-24-1555 TCGA-24-1562 
      105.99         1.18        56.58        41.06        88.50        45.50 
TCGA-24-1603 TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
       90.15         4.37         5.79        22.68        30.21        16.44 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 
       44.84       109.71        14.43        28.18        64.01        57.07 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2297 TCGA-25-1315 TCGA-25-1316 
        0.79         0.36        31.63        55.86        51.06        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
        1.02        65.00        36.95         2.99         2.96        18.58 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 TCGA-25-2391 
       20.61         0.30        56.94        60.59        14.96        49.05 
TCGA-25-2393 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
       38.04        19.99         2.96        29.03        31.00        78.90 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
      101.79        38.53        33.70        18.25        41.98        34.62 
TCGA-29-1762 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 
       85.68        24.36        22.55        11.84         8.38        34.62 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 
       62.47         4.90        11.84         9.76        38.07        51.91 
TCGA-30-1857 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 
        0.26        48.79        45.57        30.18        22.49         6.71 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1581 TCGA-36-2529 
       44.12        28.77        21.53        22.55        24.69        35.05 
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-36-2543 TCGA-36-2545 TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-57-1582 
        2.24        18.31        26.04        42.02         7.46        24.03 
TCGA-57-1585 TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 
        1.74        29.00        80.12        22.32        34.39         2.14 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 
       20.52        11.11        20.94        31.43        18.54        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1901 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 
       44.84         2.43        11.41        37.05        42.51        56.61 
TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       15.75         2.01         5.52        14.50         4.01        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
        1.18        45.96         4.80        51.72        71.74        61.64 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2113 
       58.39        65.52        55.50         6.48        20.68        22.22 
TCGA-VG-A8LO 
        0.79 

  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                           0.36                            0.26 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                         180.20                          112.41 
  AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE 
                          25.87                           29.98 
[1] "0.4 - 180.2 (25.9)" "0.3 - 112.4 (30.0)"
[1] "hr=" "1"  
D17V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 17(12P13.33) MUTATED         2   317                1
  AMP PEAK 17(12P13.33) WILD-TYPE       0   240                1
D17V3, multiclass
                  clus
vv                 AMP PEAK 17(12P13.33) MUTATED
  OMENTUM                                      2
  OVARY                                      317
  PERITONEUM OVARY                             1
                  clus
vv                 AMP PEAK 17(12P13.33) WILD-TYPE
  OMENTUM                                        0
  OVARY                                        240
  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, continuous
D17V5, binary
                                 cls
clus                                0   1
  AMP PEAK 17(12P13.33) MUTATED     2 325
  AMP PEAK 17(12P13.33) WILD-TYPE   1 243
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 17(12P13.33) MUTATED      2  325
  AMP PEAK 17(12P13.33) WILD-TYPE    1  243
     clus
vv    AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE
  NO                              2                               1
  YES                           325                             243
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 17(12P13.33) MUTATED    9 12  4  3
  AMP PEAK 17(12P13.33) WILD-TYPE  5 14  1  0
D17V6, multiclass
    clus
vv   AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE
  R0                             9                               5
  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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(12P13.33) MUTATED                                  2    10
  AMP PEAK 17(12P13.33) WILD-TYPE                                1     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(12P13.33) MUTATED                          18
  AMP PEAK 17(12P13.33) WILD-TYPE                        14
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 17(12P13.33) MUTATED                                           1
  AMP PEAK 17(12P13.33) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 17(12P13.33) MUTATED     271
  AMP PEAK 17(12P13.33) WILD-TYPE   204
D17V7, multiclass
                                           clus
vv                                          AMP PEAK 17(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               271
                                           clus
vv                                          AMP PEAK 17(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        1
  ASIAN                                                                   8
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 204
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                                 cls
clus                                0   1
  AMP PEAK 17(12P13.33) MUTATED     5 174
  AMP PEAK 17(12P13.33) WILD-TYPE   5 151
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 17(12P13.33) MUTATED      5  174
  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                           174
                        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   136 164
  AMP PEAK 18(12P12.1) WILD-TYPE 130 126
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           300                            256 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                           164                            126 
$`AMP PEAK 18(12P12.1) MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 
       41.00        46.62        18.51        65.52        63.09        65.46 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       49.28        44.32        82.39        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 
      119.08        29.10        84.20        27.88        36.23        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       45.37        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 
        9.99        38.43        41.62        61.87        55.36        17.98 
TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2049 TCGA-09-2051 
        5.85         8.55         6.18         6.12       112.41        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       39.75        12.46        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0727 
       32.28        11.70        19.86        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 
       32.25        31.04        36.72        30.35        19.59         8.12 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.19        43.86        13.61        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0899 TCGA-13-0901 TCGA-13-0904 
       66.67        70.39        67.99        56.15        19.36        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-1411 
       47.84        44.94        21.17        13.81         6.41         4.21 
TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-13-1494 
       87.06        98.04        20.68        70.82        82.88        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 
       49.25         4.24        54.31        38.40        16.57         4.21 
TCGA-13-1506 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.41         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-1682 
       10.78         8.75         6.28        54.77         8.42        27.52 
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        42.54 
TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 
       15.39        29.13         2.24         3.22        68.68         4.57 
TCGA-23-1118 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
       86.01         6.38        39.09        33.47        58.13         0.53 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0982 
       91.66        77.00         4.70         4.50        19.66        22.32 
TCGA-24-1105 TCGA-24-1418 TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 
       47.41         7.99         0.76         6.02         4.83        18.67 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
        8.55        45.14         9.11        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       64.27        16.21        58.09        39.88        19.53        44.09 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 
       47.70        25.87        10.26        17.23        88.37        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 
       38.24         8.32         3.72         3.81        11.28         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 
        9.80        30.21        11.05        81.11         4.87       152.02 
TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       18.48        44.52        36.16        70.45        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 
       67.36        36.23        16.64        33.11        53.26         1.02 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 
       26.96        51.06        34.98        36.95        33.96        12.00 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
        2.96        18.02        15.81         0.36        20.61         7.86 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.54        51.22        14.96        24.99        18.05        85.05 
TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 
       13.02         1.02        38.04         3.02        45.01        42.02 
TCGA-25-2404 TCGA-25-2409 TCGA-29-1690 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       29.03        26.99        44.71         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 
        0.53        18.67        29.23        17.00        66.81        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 
       31.23        22.98        17.33        12.36        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 
        8.38         7.23         5.36        86.17        65.00        45.11 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       11.84        11.47        21.04        51.91        36.26         2.47 
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-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       24.26        30.05        18.77         6.71        42.51         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 
       29.10        22.85         8.55        30.08        24.23        35.05 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       21.60         2.24        14.17         6.05        16.18        11.47 
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-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 
       25.02       180.20       116.12         9.40        34.39         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       44.81         8.09        27.88         4.34        31.79        28.47 
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-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 
       13.02         9.07        34.13        31.30        67.76        43.43 
TCGA-61-1919 TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 
       38.17        17.98        39.85        30.64         1.18        45.40 
TCGA-61-2088 TCGA-61-2097 TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
        4.77        60.62         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         8.05 

$`AMP PEAK 18(12P12.1) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 TCGA-04-1348 
       40.24         1.81        49.15         2.01        11.87        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       21.57        63.98        32.52        33.67        76.57        71.47 
TCGA-04-1514 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 
       56.55        55.43        48.89        28.64        64.64        47.70 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 
       89.33        74.93        57.60        30.51         3.02        97.55 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 
       35.15         4.54        71.11        20.94        26.93        54.31 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 
        3.91        35.44        35.80        15.12         6.21        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 
        2.73        12.39        31.10        34.06        21.40         8.45 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 
       38.93        28.70         8.71         7.79         8.28        35.28 
TCGA-13-0805 TCGA-13-0886 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       35.28        74.27        61.84        69.01        43.36        57.47 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       57.07        47.38        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       29.98        14.89         4.64         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        7.36         6.05         5.92         6.84         4.70         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 
       54.64        61.71        29.42        22.39        52.44        73.55 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       37.61        13.97        32.84         4.77         4.18         2.56 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-23-1023 
       23.05        25.94        26.20        72.20        25.38        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 
       26.83        31.76        49.41         8.81        18.90        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-2072 
       54.51        31.20        33.30       129.96         4.27        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 
      115.89        87.48        49.84         2.76         7.63        11.64 
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-24-1417 TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1426 
        6.38         7.82         7.86         6.25         5.95         5.36 
TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
       17.39        28.37        19.17        43.53        72.92        12.46 
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-24-1556 TCGA-24-1562 TCGA-24-1603 TCGA-24-1843 
       41.39        88.50        70.62        45.50        90.15         3.48 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2023 TCGA-24-2024 
        4.37         5.79        22.68        16.44        44.84        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       34.82       109.71        14.43        53.95        28.18        64.01 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2297 
       57.07         0.79         0.36        47.54        31.63        55.86 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1319 TCGA-25-1322 TCGA-25-1623 
       32.02        37.02         1.02        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        56.94        60.59        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        47.18       101.79        38.53 
TCGA-29-1696 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       33.70        16.90        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 
       85.68        62.93        24.36        22.55        11.84        34.62 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1714 TCGA-30-1856 
       62.47         4.90        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-3P-A9WA TCGA-42-2582 
       23.80        20.98        18.31        20.52         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 
       23.74         9.44        42.02         7.46        40.77        21.14 
TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2355 TCGA-59-A5PD TCGA-61-1721 
       29.00        80.12        22.32         2.14        20.52        11.11 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       20.94        31.43        18.54        48.79        44.84        35.80 
TCGA-61-1901 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 
       11.41        37.05        42.51        48.92        56.61        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2017 
        2.01         5.52        14.50         4.01        30.64        45.96 
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-61-2104 TCGA-61-2109 TCGA-VG-A8LO 
       55.50        76.87        20.68         0.79 

  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                         129.96 
  AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE 
                        25.005                         30.080 
[1] "0.3 - 180.2 (25.0)" "0.3 - 130.0 (30.1)"
[1] "hr=" "1.2"
D18V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 18(12P12.1) MUTATED         2   300                2
  AMP PEAK 18(12P12.1) WILD-TYPE       0   257                0
D18V3, multiclass
                  clus
vv                 AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     300                            257
  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, continuous
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(12P12.1) MUTATED     1 310
  AMP PEAK 18(12P12.1) WILD-TYPE   2 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12P12.1) MUTATED      1  310
  AMP PEAK 18(12P12.1) WILD-TYPE    2  258
     clus
vv    AMP PEAK 18(12P12.1) MUTATED AMP PEAK 18(12P12.1) WILD-TYPE
  NO                             1                              2
  YES                          310                            258
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 18(12P12.1) MUTATED    7 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                            7                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(12P12.1) MUTATED                                  3     9
  AMP PEAK 18(12P12.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(12P12.1) MUTATED                          16
  AMP PEAK 18(12P12.1) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 18(12P12.1) MUTATED                                           1
  AMP PEAK 18(12P12.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 18(12P12.1) MUTATED     258
  AMP PEAK 18(12P12.1) WILD-TYPE   217
D18V7, multiclass
                                           clus
vv                                          AMP PEAK 18(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              258
                                           clus
vv                                          AMP PEAK 18(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       0
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                217
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(12P12.1) MUTATED     5 173
  AMP PEAK 18(12P12.1) WILD-TYPE   5 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(12P12.1) MUTATED      5  173
  AMP PEAK 18(12P12.1) WILD-TYPE    5  152
                        clus
vv                       AMP PEAK 18(12P12.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          173
                        clus
vv                       AMP PEAK 18(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            152
[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    95 115
  AMP PEAK 19(12Q15) WILD-TYPE 171 175
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         210                          346 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                         115                          175 
$`AMP PEAK 19(12Q15) MUTATED`
TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
       41.00         2.01        46.62        18.51        65.52        63.09 
TCGA-04-1348 TCGA-04-1351 TCGA-04-1362 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       48.76        65.46        44.32        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1646 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       29.10        27.88        45.37        29.16         9.47        57.76 
TCGA-09-0369 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2048 
       35.57        55.36        17.98         5.85         3.02         4.54 
TCGA-09-2049 TCGA-09-2053 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
      112.41        39.75        25.91        81.47        18.51        33.24 
TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 
       35.80         6.21        24.59         2.73        15.19        17.82 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 
       21.40        36.72        30.35        19.59         8.12        35.28 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
      107.18        66.67        70.39        61.84        67.99        43.36 
TCGA-13-0901 TCGA-13-0910 TCGA-13-0911 TCGA-13-0920 TCGA-13-1407 TCGA-13-1481 
       19.36        37.08        27.72        13.81         6.05        87.06 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1496 TCGA-13-1499 TCGA-13-1505 
       98.04        20.68        70.82         4.24        38.40         4.21 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        4.41         4.18         3.91        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-A5FU TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 
        8.75         8.42        27.52        16.70         2.93        47.54 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 TCGA-23-1116 TCGA-23-1121 TCGA-23-1122 
       29.13         2.24         3.22         4.57         6.38        39.09 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-1418 
       58.13         0.53         4.70         4.50        19.66         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1434 TCGA-24-1436 
        7.86         0.76         6.02         4.83        18.67         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       12.46        45.14         9.11        22.22        26.96        57.40 
TCGA-24-1548 TCGA-24-1553 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       16.21        58.09        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 TCGA-24-1616 TCGA-24-1845 TCGA-24-1847 
       47.70        25.87        10.26        38.24         3.81        11.28 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        5.52         9.80        30.21        11.05        81.11         4.87 
TCGA-24-2020 TCGA-24-2027 TCGA-24-2033 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
      152.02       109.71        18.48        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2293 
        0.36        70.45        44.61         0.82        36.23        16.64 
TCGA-24-2295 TCGA-25-1312 TCGA-25-1315 TCGA-25-1321 TCGA-25-1323 TCGA-25-1626 
       33.11         1.02        51.06        33.96        12.00        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
        0.36        20.61        35.54        51.22        14.96        24.99 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 
        1.02        38.04        45.01        42.02        29.03        78.90 
TCGA-29-1690 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 TCGA-29-1761 TCGA-29-1763 
       44.71        68.32         0.53        18.67        17.00        66.81 
TCGA-29-1766 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 TCGA-29-2414 
       39.12        17.33        12.36        14.93         5.36        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1859 
       65.00        45.11        42.25        11.47        21.04        48.10 
TCGA-30-1866 TCGA-30-1867 TCGA-31-1950 TCGA-31-1955 TCGA-31-1959 TCGA-36-1571 
       36.62         1.22        18.77        42.51         2.20        22.85 
TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 TCGA-36-2548 TCGA-36-2551 TCGA-36-2552 
       27.85        35.05        33.01        14.17        16.18        11.47 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 
       23.74         9.44         7.46        24.03        11.38        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08        25.02       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2372 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 
        9.40        44.81         8.09         4.34        31.79         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1906 TCGA-61-1907 TCGA-61-2000 TCGA-61-2002 
       33.67        43.69        34.13        31.30        14.50        17.98 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 
       39.85        30.64         4.77        71.74        60.62        65.52 
TCGA-61-2102 TCGA-61-2111 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-WR-A838 
        6.48       125.75         6.35        31.07         8.61         8.05 

$`AMP PEAK 19(12Q15) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1343 TCGA-04-1349 TCGA-04-1350 
       40.24         1.81        49.15        11.87        21.57        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        33.67        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 
       56.55        41.59        84.20        55.43        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0367 TCGA-09-1659 
       64.64        36.23        31.86        47.70        17.98         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-09-1669 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       30.51         8.55        97.55         6.18         6.12        35.15 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        63.09        20.94        26.93        12.46        54.31 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 
       44.55        39.58        12.39        31.10        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        34.06        32.25        31.04 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
        8.45        38.93        28.70         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 
        8.19        43.86        35.28        13.61        68.94        91.40 
TCGA-13-0886 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       74.27        69.01        57.47        56.15        57.07        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 
       48.33        47.84        44.94        44.84        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 
        5.33        54.64        61.71        29.42        22.39        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        38.20        49.25        54.31        37.61 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 
       13.97        32.84        16.57         4.77         2.56         3.09 
TCGA-13-2059 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       12.23         6.28        54.77        23.05        25.94        26.20 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       72.20        25.38        19.10         2.66        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       15.39        26.83        31.76        49.41         8.81        18.90 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51        31.20        68.68        33.30        86.01 
TCGA-23-1119 TCGA-23-1120 TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 
      129.96         4.27        33.47        24.95       115.89        87.48 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0966 TCGA-24-0970 
       91.66        77.00        49.84         2.76         7.63        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-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1423 TCGA-24-1425 
       47.41         6.31         6.38         7.82         6.25         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        19.17        43.53        72.92 
TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
      105.99         3.45         1.18        64.27        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1567 TCGA-24-1603 
       51.91        41.39        88.50        70.62        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       88.37        48.33         8.32         3.48         3.72         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-24-2029 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 
       14.43        53.95        28.18        64.01        57.07        47.54 
TCGA-24-2271 TCGA-24-2289 TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 
       31.63        67.36        55.86        53.26        26.96        32.02 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 
       37.02         1.02        34.98        65.00        36.95         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
        2.96        18.58        18.02         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 
       60.59        18.05        85.05        13.02        49.05         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1691 
       12.00        19.99         2.96        31.00        26.99        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 
      101.79        38.53         0.79        33.70        31.20        16.90 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 
       59.67        18.25        41.98        29.23        34.62        85.68 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1776 
       62.93        31.23        22.98        24.36        22.55        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       12.30         8.38         7.23        34.62        62.47         4.90 
TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       11.84         9.76        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1880 
       15.68         0.26        44.91        34.78         6.12        57.57 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 
       24.26        30.05        48.79        45.57        30.18        22.49 
TCGA-31-1953 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 
        6.71        44.12        28.77        29.10        21.53        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-36-2543 
       29.82        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 
       20.98        18.31        20.52         6.05         7.99        26.04 
TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-59-2349 
       42.02        40.77         1.48        21.14         1.74        80.12 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         2.14         5.42        20.52        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 
       22.22        39.68        18.94         0.79 

  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                       129.96 
  AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE 
                       24.31                        29.90 
[1] "0.4 - 180.2 (24.3)" "0.3 - 130.0 (29.9)"
[1] "hr=" "1.2"
D19V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 19(12Q15) MUTATED         2   209                2
  AMP PEAK 19(12Q15) WILD-TYPE       0   348                0
D19V3, multiclass
                  clus
vv                 AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  OMENTUM                                   2                            0
  OVARY                                   209                          348
  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, continuous
D19V5, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED     1 219
  AMP PEAK 19(12Q15) WILD-TYPE   2 349
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      1  219
  AMP PEAK 19(12Q15) WILD-TYPE    2  349
     clus
vv    AMP PEAK 19(12Q15) MUTATED AMP PEAK 19(12Q15) WILD-TYPE
  NO                           1                            2
  YES                        219                          349
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 19(12Q15) MUTATED    5 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                          5                            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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(12Q15) MUTATED                                  1     6
  AMP PEAK 19(12Q15) WILD-TYPE                                2    12
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(12Q15) MUTATED                          14
  AMP PEAK 19(12Q15) WILD-TYPE                        18
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(12Q15) MUTATED                                           0   179
  AMP PEAK 19(12Q15) WILD-TYPE                                         1   296
D19V7, multiclass
                                           clus
vv                                          AMP PEAK 19(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              6
  BLACK OR AFRICAN AMERICAN                                         14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                            179
                                           clus
vv                                          AMP PEAK 19(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              296
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                              cls
clus                             0   1
  AMP PEAK 19(12Q15) MUTATED     4 109
  AMP PEAK 19(12Q15) WILD-TYPE   6 216
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(12Q15) MUTATED      4  109
  AMP PEAK 19(12Q15) WILD-TYPE    6  216
                        clus
vv                       AMP PEAK 19(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        109
                        clus
vv                       AMP PEAK 19(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          216
[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    65  74
  AMP PEAK 20(14Q11.2) WILD-TYPE 201 216
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                           139                            417 
  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                            74                            216 
$`AMP PEAK 20(14Q11.2) MUTATED`
TCGA-04-1332 TCGA-04-1347 TCGA-04-1356 TCGA-04-1362 TCGA-04-1514 TCGA-04-1516 
       41.00        63.09        49.28        44.32        56.55        41.59 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 TCGA-04-1652 TCGA-09-0364 TCGA-09-0367 
      119.08        29.10        27.88        31.86        29.16        17.98 
TCGA-09-1659 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1674 
        9.99        41.62        61.87        55.36        30.51         8.55 
TCGA-09-2049 TCGA-09-2053 TCGA-10-0928 TCGA-10-0933 TCGA-13-0714 TCGA-13-0724 
      112.41        39.75        18.51        11.70         6.21         2.73 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0760 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 
       17.82        55.17        11.54        32.25        21.40         8.45 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0888 TCGA-13-0891 TCGA-13-0899 
       38.93        30.35        19.59        70.39        69.01        56.15 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0911 TCGA-13-0919 TCGA-13-1408 TCGA-13-1489 
       19.36        48.33        27.72        14.89         5.92        82.88 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 
       54.31        38.40        32.84         3.91        14.24        12.23 
TCGA-20-0990 TCGA-20-0991 TCGA-23-1021 TCGA-23-1029 TCGA-23-1031 TCGA-23-1110 
       25.94        26.20        47.54         8.81        18.90        54.51 
TCGA-23-1114 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 
       68.68        33.47         0.53        24.95        87.48        49.84 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 TCGA-24-1417 TCGA-24-1424 
        4.50         7.63        19.66        41.56         7.82         6.02 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1474 TCGA-24-1545 TCGA-24-1555 TCGA-24-1557 
       12.46        45.14        22.22        57.40        88.50        39.88 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1850 TCGA-24-1923 
       88.37        38.24         8.32         3.72         5.52        22.68 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2030 TCGA-24-2281 TCGA-24-2289 TCGA-24-2298 
        4.87       152.02        53.95        44.61        67.36        53.26 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 
       26.96        32.02         1.02        34.98        33.96         2.99 
TCGA-25-1323 TCGA-25-1627 TCGA-25-1628 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       12.00         0.36        20.61        24.99        18.05        85.05 
TCGA-25-2392 TCGA-25-2400 TCGA-25-2408 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 
        1.02        42.02        31.00        68.32        16.90        18.67 
TCGA-29-1766 TCGA-29-1775 TCGA-29-1784 TCGA-29-2414 TCGA-29-2428 TCGA-29-2434 
       39.12        12.36         5.36        86.17        45.11        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 
       21.04        38.07        51.91        48.10        44.91        36.62 
TCGA-31-1959 TCGA-36-1571 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 
        2.20        22.85        30.08        27.85        24.69        35.05 
TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-57-1582 TCGA-57-1583 TCGA-59-2352 
       18.31        14.17         6.05        24.03        11.38         9.40 
TCGA-59-2355 TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 TCGA-61-1904 TCGA-61-1907 
        2.14        20.94        27.88         4.34         9.07        31.30 
TCGA-61-1917 TCGA-61-1918 TCGA-61-2009 TCGA-61-2012 TCGA-61-2097 TCGA-61-2612 
       43.43        15.75        39.85        30.64        60.62         6.35 
TCGA-WR-A838 
        8.05 

$`AMP PEAK 20(14Q11.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24         1.81        49.15         2.01        46.62        18.51 
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-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1517 
       32.52        33.67        76.57        71.47        82.39        19.99 
TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       38.37        84.20        55.43        48.89        28.64        64.64 
TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 
       36.23        47.70        45.37         9.47        57.76        35.57 
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-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       71.11        63.09        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       25.91        81.47        33.24        32.28         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       35.80        15.12        19.86        24.59        44.55        39.58 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       12.39        31.10        15.19         2.50        11.18        11.38 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       34.06        31.04        36.72        28.70         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        8.12         8.28         8.19        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 
       61.84        67.99        43.36        57.47        57.07        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 
       47.84        44.94        44.84        37.08        34.06        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         6.05         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        5.33        54.64        87.06        61.71        29.42        98.04 
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        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 
       49.25         4.24        37.61        13.97        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2060 
        4.41         4.77         4.18         2.56         3.09         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         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        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 
       49.41        29.13         2.24        51.35         3.22        31.20 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 
        4.57        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        19.17        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 
       51.06        37.02        65.00        36.95         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       18.02        15.81         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       35.54        51.22        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        44.71        47.18       101.79        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 
        0.79        33.70        31.20         0.53        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        29.23        34.62        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        31.23        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        34.62 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       65.00        62.47         4.90        42.25        11.84         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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        7.46        40.77         1.48        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
       29.00        25.08        25.02       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
      116.12        34.39         5.42        44.81        20.52        11.11 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
        8.09        31.43        18.54        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-61-1910 
        8.42         5.79        11.41        13.02        34.13        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 
       42.51        48.92        56.61        67.76        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 
        5.52        14.50        17.98         4.01        30.64         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-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       61.64        58.39        65.52        55.50         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 
       20.68        44.52       125.75        22.22        31.07         8.61 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

  AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE 
                          0.36                           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 
                         27.88                          28.37 
[1] "0.4 - 152.0 (27.9)" "0.3 - 180.2 (28.4)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 20(14Q11.2) MUTATED         0   142                2
  AMP PEAK 20(14Q11.2) WILD-TYPE       2   415                0
D20V3, multiclass
                  clus
vv                 AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     142                            415
  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, continuous
D20V5, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q11.2) MUTATED     2 144
  AMP PEAK 20(14Q11.2) WILD-TYPE   1 424
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q11.2) MUTATED      2  144
  AMP PEAK 20(14Q11.2) WILD-TYPE    1  424
     clus
vv    AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE
  NO                             2                              1
  YES                          144                            424
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 20(14Q11.2) MUTATED    4  6  0  0
  AMP PEAK 20(14Q11.2) WILD-TYPE 10 20  5  3
D20V6, multiclass
    clus
vv   AMP PEAK 20(14Q11.2) MUTATED AMP PEAK 20(14Q11.2) WILD-TYPE
  R0                            4                             10
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(14Q11.2) MUTATED                                  0     4
  AMP PEAK 20(14Q11.2) WILD-TYPE                                3    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(14Q11.2) MUTATED                           6
  AMP PEAK 20(14Q11.2) WILD-TYPE                        26
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(14Q11.2) MUTATED                                           1
  AMP PEAK 20(14Q11.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 20(14Q11.2) MUTATED     122
  AMP PEAK 20(14Q11.2) WILD-TYPE   353
D20V7, multiclass
                                           clus
vv                                          AMP PEAK 20(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              122
                                           clus
vv                                          AMP PEAK 20(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                353
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q11.2) MUTATED     5  84
  AMP PEAK 20(14Q11.2) WILD-TYPE   5 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q11.2) MUTATED      5   84
  AMP PEAK 20(14Q11.2) WILD-TYPE    5  241
                        clus
vv                       AMP PEAK 20(14Q11.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       AMP PEAK 20(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            241
[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    76  72
  AMP PEAK 21(14Q32.33) WILD-TYPE 190 218
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                            148                             408 
  AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE 
                             72                             218 
$`AMP PEAK 21(14Q32.33) MUTATED`
TCGA-04-1338 TCGA-04-1350 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 
       46.62        63.98        76.57        71.47        56.55        19.99 
TCGA-04-1644 TCGA-04-1646 TCGA-09-0369 TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 
       48.89        27.88        35.57        89.33        41.62        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-10-0931 
       55.36        30.51        97.55         6.12        35.15        32.28 
TCGA-10-0933 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0723 TCGA-13-0762 
       11.70        15.12         6.21        24.59        39.58        32.25 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0801 TCGA-13-0803 TCGA-13-0886 
       21.40         8.45        38.93         8.28        43.86        74.27 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       70.39        67.99        43.36        56.15        57.07        19.36 
TCGA-13-0905 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-1408 
       47.84        34.06        21.17        14.89        13.81         5.92 
TCGA-13-1412 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 TCGA-13-1509 TCGA-13-2057 
        5.33        54.31        32.84         4.21         4.18        14.24 
TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0991 TCGA-23-1021 
        8.61        10.78        54.77         8.42        26.20        47.54 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1124 
       49.41         8.81         4.57        33.30        86.01        58.13 
TCGA-23-1809 TCGA-23-2078 TCGA-23-2081 TCGA-24-0975 TCGA-24-1103 TCGA-24-1105 
        0.53        87.48        77.00        21.80        54.12        47.41 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1427 TCGA-24-1435 TCGA-24-1474 TCGA-24-1545 
        7.86         0.76         4.83        43.53        22.22        57.40 
TCGA-24-1546 TCGA-24-1555 TCGA-24-1557 TCGA-24-1842 TCGA-24-1844 TCGA-24-1923 
       64.27        88.50        39.88         8.32         3.72        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2030 
       30.21        16.44        81.11         4.87        44.84        53.95 
TCGA-24-2035 TCGA-24-2261 TCGA-24-2280 TCGA-24-2281 TCGA-25-1313 TCGA-25-1314 
       28.18         0.79        70.45        44.61        26.96        32.02 
TCGA-25-1317 TCGA-25-1322 TCGA-25-2392 TCGA-25-2400 TCGA-25-2401 TCGA-25-2408 
        1.02         2.99         1.02        42.02         2.96        31.00 
TCGA-29-1688 TCGA-29-1691 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 
       78.90        47.18        31.20        16.90        18.67        18.25 
TCGA-29-1707 TCGA-29-1762 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1784 
       41.98        85.68        24.36        12.36        11.84         5.36 
TCGA-29-2428 TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1860 TCGA-30-1866 
       45.11        11.47        38.07        36.26        44.91        36.62 
TCGA-31-1951 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1577 TCGA-36-1581 
       22.49         2.20        29.10        21.53        25.74        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2551 
       35.05        33.01         2.24        18.31        20.52        16.18 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
       26.04         9.44         7.46        24.03        11.38        21.14 
TCGA-59-2348 TCGA-59-2355 TCGA-61-1725 TCGA-61-1730 TCGA-61-1740 TCGA-61-1900 
      180.20         2.14        31.43         4.34         2.43         5.79 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-2012 
       13.02        31.30        67.76        15.75        38.17        30.64 
TCGA-61-2097 TCGA-61-2109 TCGA-61-2612 TCGA-WR-A838 
       60.62        20.68         6.35         8.05 

$`AMP PEAK 21(14Q32.33) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       40.24        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
       11.87        65.52        63.09        48.76        21.57        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 
       49.28        32.52        44.32        33.67        82.39        41.59 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 
       38.37       119.08        29.10        84.20        55.43        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 
       64.64        36.23        31.86        47.70        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 
        9.47        57.76        17.98         9.99        38.43        74.93 
TCGA-09-1666 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 
       57.60        17.98         5.85         3.02         8.55         6.18 
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-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0720 
       33.24         3.91        35.44        35.80        19.86        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
        2.73        12.39        31.10        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 
        2.50        11.18        11.38        11.54        34.06        31.04 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       36.72        28.70        30.35        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.12         8.19        35.28        35.28        13.61        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 
      107.18        91.40        66.67        61.84        69.01        57.47 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        48.33        44.94        44.84        37.08        27.72 
TCGA-13-0913 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       29.98         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 
        7.36         6.05         6.84         4.70         4.21        54.64 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 
       87.06        61.71        29.42        98.04        20.68        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 
        4.24        37.61        38.40        13.97        16.57         4.41 
TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2065 
        4.77         2.56         3.91         3.09        12.23         8.75 
TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
        6.28        23.05        25.94        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       19.10        16.70         2.93         2.66        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       15.39        26.83        31.76        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1119 
       51.35        54.51         3.22        31.20        68.68       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-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       91.66        49.84         2.76         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
       19.66        11.64        41.56         7.66        22.32        63.55 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1424 
        6.31         6.38         7.82         7.99         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        19.17        18.67 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        8.55        72.92        12.46        45.14       105.99         9.11 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
        3.45         1.18        26.96        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 
       51.91        41.39        58.09        70.62        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-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       88.37        48.33        38.24         3.48         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1928 TCGA-24-2020 
       11.28         5.79         5.52         9.80        11.05       152.02 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 
       58.16        34.82       109.71        14.43        18.48        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07        36.16         0.36        47.54        31.63 
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-25-1315 TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 
       53.26         1.02        51.06        37.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       36.95        33.96        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       85.05        13.02        49.05        38.04         3.02        12.00 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2409 TCGA-29-1690 TCGA-29-1693 
       45.01        19.99        29.03        26.99        44.71       101.79 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 
       38.53         0.79        33.70        68.32         0.53        59.67 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       29.23        34.62        17.00        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 TCGA-29-1778 
       31.23        22.98        22.55        17.33        12.30        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
        8.38         7.23        34.62        86.17        65.00        62.47 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 
        4.90        42.25        11.84         9.76        21.04        51.91 
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-30-1867 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-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       30.18        18.77         6.71        42.51        44.12        28.77 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        30.08        27.85        24.23 
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-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 
       20.98        14.17         6.05        11.47         7.99        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-59-A5PD TCGA-61-1721 TCGA-61-1722 
       34.39         5.42        44.81        20.52        11.11         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       20.94        18.54        27.88        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80        33.67        43.69         1.45         8.42 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 
       11.41         9.07        34.13        37.05        42.51        48.92 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       56.61        43.43         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-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       65.52        55.50         6.48        76.87        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22        31.07         8.61        39.68        18.94         0.79 

  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 
                         28.030                          28.125 
[1] "0.5 - 180.2 (28.0)" "0.3 - 152.0 (28.1)"
[1] "hr=" "1.1"
D21V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 21(14Q32.33) MUTATED         0   151                1
  AMP PEAK 21(14Q32.33) WILD-TYPE       2   406                1
D21V3, multiclass
                  clus
vv                 AMP PEAK 21(14Q32.33) MUTATED
  OMENTUM                                      0
  OVARY                                      151
  PERITONEUM OVARY                             1
                  clus
vv                 AMP PEAK 21(14Q32.33) WILD-TYPE
  OMENTUM                                        2
  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, continuous
D21V5, binary
                                 cls
clus                                0   1
  AMP PEAK 21(14Q32.33) MUTATED     3 152
  AMP PEAK 21(14Q32.33) WILD-TYPE   0 416
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(14Q32.33) MUTATED      3  152
  AMP PEAK 21(14Q32.33) WILD-TYPE    0  416
     clus
vv    AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE
  NO                              3                               0
  YES                           152                             416
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 21(14Q32.33) MUTATED    4  8  2  1
  AMP PEAK 21(14Q32.33) WILD-TYPE 10 18  3  2
D21V6, multiclass
    clus
vv   AMP PEAK 21(14Q32.33) MUTATED AMP PEAK 21(14Q32.33) WILD-TYPE
  R0                             4                              10
  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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(14Q32.33) MUTATED                                  0     5
  AMP PEAK 21(14Q32.33) WILD-TYPE                                3    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(14Q32.33) MUTATED                          11
  AMP PEAK 21(14Q32.33) WILD-TYPE                        21
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 21(14Q32.33) MUTATED                                           0
  AMP PEAK 21(14Q32.33) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  AMP PEAK 21(14Q32.33) MUTATED     126
  AMP PEAK 21(14Q32.33) WILD-TYPE   349
D21V7, multiclass
                                           clus
vv                                          AMP PEAK 21(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               126
                                           clus
vv                                          AMP PEAK 21(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 349
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                                 cls
clus                                0   1
  AMP PEAK 21(14Q32.33) MUTATED     3  81
  AMP PEAK 21(14Q32.33) WILD-TYPE   7 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(14Q32.33) MUTATED      3   81
  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                            81
                        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    81  75
  AMP PEAK 22(15Q26.3) WILD-TYPE 185 215
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                           156                            400 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                            75                            215 
$`AMP PEAK 22(15Q26.3) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       40.24        49.15        63.09        65.46        49.28        32.52 
TCGA-04-1362 TCGA-04-1516 TCGA-04-1644 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 
       44.32        41.59        48.89        17.98        35.57        89.33 
TCGA-09-1665 TCGA-09-1669 TCGA-09-1674 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
       41.62        30.51         8.55       112.41        63.09        39.75 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       18.51        33.24        32.28         3.91        35.44        15.12 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0792 TCGA-13-0797 TCGA-13-0802 TCGA-13-0884 
       34.06        31.04        36.72         8.71         8.19       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0890 TCGA-13-0897 TCGA-13-0903 TCGA-13-0906 
       91.40        66.67        67.99        57.47        47.38        44.94 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 
       21.17        14.89         6.41         6.61         6.05         5.92 
TCGA-13-1481 TCGA-13-1483 TCGA-13-1489 TCGA-13-1495 TCGA-13-1501 TCGA-13-1512 
       87.06        29.42        82.88        49.25        32.84         3.09 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-20-1686 
       12.23         8.61        10.78         8.75         6.28         2.93 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 
       47.54        42.54        31.76        49.41         8.81        18.90 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1118 TCGA-23-1122 TCGA-23-1124 TCGA-23-2072 
       54.51        68.68        86.01        39.09        58.13        24.95 
TCGA-23-2079 TCGA-24-0966 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 TCGA-24-1419 
       91.66         7.63        21.80        54.12         6.31         7.86 
TCGA-24-1423 TCGA-24-1428 TCGA-24-1436 TCGA-24-1466 TCGA-24-1470 TCGA-24-1546 
        6.25        17.39         8.55        45.14         3.45        64.27 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 TCGA-24-1847 
       51.91        58.09        70.62        19.53        47.70        11.28 
TCGA-24-1849 TCGA-24-2027 TCGA-24-2033 TCGA-24-2267 TCGA-24-2288 TCGA-24-2289 
        5.79       109.71        18.48        47.54         0.82        67.36 
TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-25-1313 TCGA-25-1319 TCGA-25-1321 
       36.23        33.11        55.86        26.96        65.00        33.96 
TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 TCGA-25-2391 TCGA-29-1688 
       18.02         0.36         7.86        56.94        49.05        78.90 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1707 TCGA-29-1761 
       47.18       101.79        38.53        33.70        41.98        17.00 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1775 TCGA-29-1776 TCGA-29-1781 TCGA-30-1718 
       31.23        22.98        12.36        11.84         8.38        51.91 
TCGA-30-1853 TCGA-30-1861 TCGA-31-1944 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       36.26        34.78        45.57        42.51        44.12         2.20 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1580 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 
       22.85         8.55        24.23        29.82        25.08        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-42-2587 TCGA-57-1582 TCGA-57-1992 
       20.98        18.31        20.52        23.74        24.03        29.00 
TCGA-57-1994 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1727 TCGA-61-1730 
       25.02         9.40         5.42        44.81        18.54         4.34 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
       35.80         2.43        11.41        13.02        31.30        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-2009 TCGA-61-2018 
       42.51        67.76        15.75        38.17        39.85        45.40 
TCGA-61-2096 TCGA-61-2097 TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       58.39        60.62        20.68        31.07         0.79         8.05 

$`AMP PEAK 22(15Q26.3) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81         2.01        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1364 TCGA-04-1365 
       65.52        48.76        21.57        63.98        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       71.47        82.39        56.55        19.99        38.37       119.08 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 
       29.10        84.20        55.43        27.88        28.64        64.64 
TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 
       57.76         9.99        38.43        74.93        57.60        61.87 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       55.36        17.98         5.85         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
        6.12        35.15         4.54        71.11        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0936 
       12.46        54.31        25.91        81.47        11.70        35.80 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         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        31.10        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        32.25        21.40         8.45 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 
       38.93        28.70        30.35        19.59         7.79         8.12 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        8.28        43.86        35.28        35.28        13.61        68.94 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 
       74.27        70.39        61.84        69.01        43.36        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 
       57.07        19.36        48.33        47.84        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 
       27.72        34.06        29.98        13.81         4.64         6.08 
TCGA-13-1403 TCGA-13-1405 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
       10.88         7.36         6.84         4.70         4.21         5.33 
TCGA-13-1477 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
       54.64        61.71        98.04        20.68        22.39        70.82 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       52.44        73.55        38.20         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        13.97        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-A5FT TCGA-13-A5FU 
        4.18         2.56         3.91        14.24        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       19.10        16.70         2.66        40.54        15.39        26.83 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       29.13         2.24        51.35         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 
       33.30       129.96         4.27         6.38        33.47         0.53 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        77.00        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50        19.66        11.64        41.56         7.66        22.32 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 
       63.55        47.41         6.38         7.82         7.99         0.76 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 
        6.02         5.95         5.36         4.83        28.37        19.17 
TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 
       18.67        43.53        72.92        12.46       105.99         9.11 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 
       41.06        41.39        88.50        39.88        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-24-1845 TCGA-24-1846 
       38.24         8.32         3.48         3.72         3.81         4.37 
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-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        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        53.95        28.18        64.01        44.52        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       36.16         0.79         0.36        31.63        70.45        44.61 
TCGA-24-2293 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       16.64        53.26         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
        1.02        34.98        36.95         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 
       18.58        15.81        20.61         0.30        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       51.22        14.96        24.99        18.05        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-25-2409 TCGA-29-1690 
       42.02         2.96        29.03        31.00        26.99        44.71 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
        0.79        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 
       59.67        18.25        29.23        34.62        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 
       62.93        39.12        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        34.62        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         4.90        42.25        11.84        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
        9.76        21.04        38.07         2.47        15.68         0.26 
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-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       24.26        30.05        48.79        30.18        18.77        22.49 
TCGA-31-1953 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1576 
        6.71        28.77        29.10        21.53        22.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 
       25.74        27.85        24.69        35.05        33.01        29.49 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       25.91        23.80         2.24        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       11.47         7.99        26.04         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
       40.77         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2354 
       25.08       180.20        80.12        22.32       116.12        34.39 
TCGA-59-2355 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
        2.14        20.52        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 
        6.35         8.61        39.68        18.94 

  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                          0.36                           0.26 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                        112.41                         180.20 
  AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE 
                         32.40                          26.12 
[1] "0.4 - 112.4 (32.4)" "0.3 - 180.2 (26.1)"
[1] "hr=" "1.3"
D22V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 22(15Q26.3) MUTATED         1   157                0
  AMP PEAK 22(15Q26.3) WILD-TYPE       1   400                2
D22V3, multiclass
                  clus
vv                 AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     157                            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, continuous
D22V5, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED     0 159
  AMP PEAK 22(15Q26.3) WILD-TYPE   3 409
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED      0  159
  AMP PEAK 22(15Q26.3) WILD-TYPE    3  409
     clus
vv    AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  NO                             0                              3
  YES                          159                            409
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 22(15Q26.3) MUTATED    5  8  1  0
  AMP PEAK 22(15Q26.3) WILD-TYPE  9 18  4  3
D22V6, multiclass
    clus
vv   AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
  R0                            5                              9
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(15Q26.3) MUTATED                                  0     4
  AMP PEAK 22(15Q26.3) WILD-TYPE                                3    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(15Q26.3) MUTATED                           8
  AMP PEAK 22(15Q26.3) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(15Q26.3) MUTATED                                           1
  AMP PEAK 22(15Q26.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 22(15Q26.3) MUTATED     136
  AMP PEAK 22(15Q26.3) WILD-TYPE   339
D22V7, multiclass
                                           clus
vv                                          AMP PEAK 22(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              136
                                           clus
vv                                          AMP PEAK 22(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                339
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(15Q26.3) MUTATED     3  87
  AMP PEAK 22(15Q26.3) WILD-TYPE   7 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(15Q26.3) MUTATED      3   87
  AMP PEAK 22(15Q26.3) WILD-TYPE    7  238
                        clus
vv                       AMP PEAK 22(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       AMP PEAK 22(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            238
[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    99 110
  AMP PEAK 23(17Q25.3) WILD-TYPE 167 180
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           209                            347 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                           110                            180 
$`AMP PEAK 23(17Q25.3) MUTATED`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1347 TCGA-04-1356 
       40.24         2.01        46.62        18.51        63.09        49.28 
TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 
       44.32        76.57        71.47        56.55        38.37       119.08 
TCGA-04-1536 TCGA-04-1638 TCGA-04-1652 TCGA-09-0364 TCGA-09-0369 TCGA-09-1662 
       29.10        55.43        31.86        29.16        35.57        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1675 TCGA-09-2044 
       41.62        57.60        55.36        30.51        97.55         6.12 
TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 TCGA-10-0925 TCGA-10-0931 TCGA-10-0936 
       35.15        63.09        39.75        54.31        32.28        35.80 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 TCGA-13-0760 
        6.21        24.59         2.73        17.82        55.17        11.54 
TCGA-13-0761 TCGA-13-0768 TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0807 
       34.06         8.45        30.35         8.12        43.86        13.61 
TCGA-13-0886 TCGA-13-0890 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       74.27        67.99        57.47        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0913 TCGA-13-0920 TCGA-13-0921 TCGA-13-1403 
       47.84        44.84        29.98        13.81         4.64        10.88 
TCGA-13-1404 TCGA-13-1408 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.61         5.92         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 
       61.71        29.42        22.39        70.82        82.88        49.25 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 
       37.61        13.97         4.77         4.18         2.56         3.09 
TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-1685 
       14.24         8.61         8.75         6.28         8.42        16.70 
TCGA-23-1026 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1117 
       26.83         8.81        29.13        51.35        54.51        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
       86.01       129.96         6.38        58.13        24.95       115.89 
TCGA-23-2078 TCGA-23-2081 TCGA-23-2643 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       87.48        77.00         4.70         7.63        11.64        21.80 
TCGA-24-1413 TCGA-24-1424 TCGA-24-1425 TCGA-24-1428 TCGA-24-1430 TCGA-24-1435 
        6.31         6.02         5.95        17.39        28.37        43.53 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1549 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       12.46       105.99        56.58        41.39        88.50        70.62 
TCGA-24-1563 TCGA-24-1567 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 
       47.70        17.23        48.33         8.32         3.72         3.81 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1924 TCGA-24-2020 TCGA-24-2024 TCGA-24-2029 
        5.79         5.52        30.21       152.02        58.16        14.43 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
       28.18        64.01        47.54        70.45        44.61        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 
       36.23        16.64        53.26        26.96        51.06        65.00 
TCGA-25-1320 TCGA-25-1630 TCGA-25-1632 TCGA-25-1877 TCGA-25-2392 TCGA-25-2396 
       36.95         7.86        56.94        18.05         1.02         3.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 
       19.99        42.02        29.03        78.90       101.79        38.53 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1763 
        0.79        31.20         0.53        16.90        18.25        66.81 
TCGA-29-1764 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 
       62.93        22.98        24.36        11.84         8.38        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2429 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 
       86.17        65.00         4.90        11.84        38.07        51.91 
TCGA-30-1855 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-31-1944 
        2.47        44.91         6.12        36.62        24.26        45.57 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1578 TCGA-36-1581 
       28.77        29.10        21.53        22.55        27.85        24.69 
TCGA-36-2529 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       35.05        25.91        25.08        21.60         2.24        20.98 
TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
       20.52        16.18        11.47        26.04         9.44        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1585 TCGA-57-1586 TCGA-59-2348 TCGA-59-2354 
        7.46         1.48         1.74        22.32       180.20        34.39 
TCGA-59-2355 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1725 TCGA-61-1737 TCGA-61-1738 
        2.14        20.52         8.09        31.43        44.84        35.80 
TCGA-61-1740 TCGA-61-1900 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 
        2.43         5.79        37.05        48.92        56.61        43.43 
TCGA-61-1919 TCGA-61-2098 TCGA-61-2101 TCGA-61-2612 TCGA-VG-A8LO 
       38.17        65.52        55.50         6.35         0.79 

$`AMP PEAK 23(17Q25.3) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 
       41.00         1.81        49.15        11.87        65.52        48.76 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1371 
       21.57        63.98        65.46        32.52        33.67        82.39 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1542 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 
       41.59        19.99        84.20        48.89        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 
       64.64        36.23        47.70        45.37         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1667 TCGA-09-1670 
       17.98         9.99        38.43        74.93        61.87        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2049 
        5.85         3.02         8.55         6.18         4.54       112.41 
TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 
       71.11        20.94        26.93        12.46        25.91        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 
       18.51        33.24        11.70         3.91        35.44        15.12 
TCGA-10-0938 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       19.86        44.55        39.58        12.39        31.10        15.19 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.38        32.25        31.04        21.40 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        19.59         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 
        8.28         8.19        35.28        35.28        68.94       107.18 
TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       91.40        66.67        70.39        61.84        69.01        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       56.15        57.07        44.94        37.08        27.72        34.06 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0923 TCGA-13-0924 TCGA-13-1405 TCGA-13-1407 
       21.17        14.89         6.41         6.08         7.36         6.05 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1484 TCGA-13-1485 TCGA-13-1491 TCGA-13-1492 
        6.84         4.70        98.04        20.68        52.44        73.55 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 
       38.20         4.24        54.31        38.40        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FT 
        4.21         4.41         3.91        12.23        10.78        54.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       19.10         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1111 
       15.39        31.76        49.41        18.90         2.24         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
       31.20        68.68         4.57         4.27        39.09        33.47 
TCGA-23-1809 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0968 
        0.53        91.66        49.84         2.76         4.50        19.66 
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-24-1416 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-24-1426 TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
        5.36         4.83        19.17        18.67         8.55        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         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-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 
       39.88        19.53        44.09        45.50        25.87        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1846 TCGA-24-1847 
       90.15        88.37        38.24         3.48         4.37        11.28 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        9.80        22.68        16.44        11.05        81.11         4.87 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2038 
       44.84        34.82       109.71        53.95        18.48        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 
       57.07        36.16         0.79         0.36        31.63         0.82 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 
       33.11        55.86         1.02        32.02        37.02         1.02 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       34.98        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 
       18.02        15.81         0.36        20.61         0.30        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 
       35.54        51.22        14.96        24.99        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-25-2408 
       49.05        38.04        12.00        45.01         2.96        31.00 
TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1696 TCGA-29-1698 TCGA-29-1702 
       26.99        44.71        47.18        33.70        68.32        18.67 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       59.67        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.12        31.23        22.55        17.33        12.36        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 
       14.93         7.23         5.36        62.47        45.11        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
       11.47         9.76        21.04        36.26        15.68         0.26 
TCGA-30-1859 TCGA-30-1861 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       48.10        34.78         1.22        57.57        30.05        48.79 
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-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
        2.20        22.85         8.55        30.08        25.74        24.23 
TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 TCGA-36-2540 TCGA-36-2545 TCGA-36-2548 
       33.01        29.49        29.82        23.80        18.31        14.17 
TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
        6.05         7.99        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 
       31.07         8.61        39.68        18.94         8.05 

  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                          0.53                           0.26 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                        180.20                         125.75 
  AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE 
                         29.42                          25.94 
[1] "0.5 - 180.2 (29.4)" "0.3 - 125.8 (25.9)"
[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       0   350                1
D23V3, multiclass
                  clus
vv                 AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     207                            350
  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, continuous
D23V5, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED     1 211
  AMP PEAK 23(17Q25.3) WILD-TYPE   2 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED      1  211
  AMP PEAK 23(17Q25.3) WILD-TYPE    2  357
     clus
vv    AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  NO                             1                              2
  YES                          211                            357
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 23(17Q25.3) MUTATED    4 14  4  0
  AMP PEAK 23(17Q25.3) WILD-TYPE 10 12  1  3
D23V6, multiclass
    clus
vv   AMP PEAK 23(17Q25.3) MUTATED AMP PEAK 23(17Q25.3) WILD-TYPE
  R0                            4                             10
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(17Q25.3) MUTATED                                  2     6
  AMP PEAK 23(17Q25.3) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(17Q25.3) MUTATED                          14
  AMP PEAK 23(17Q25.3) WILD-TYPE                        18
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(17Q25.3) MUTATED                                           0
  AMP PEAK 23(17Q25.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 23(17Q25.3) MUTATED     176
  AMP PEAK 23(17Q25.3) WILD-TYPE   299
D23V7, multiclass
                                           clus
vv                                          AMP PEAK 23(17Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              176
                                           clus
vv                                          AMP PEAK 23(17Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                299
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q25.3) MUTATED     4 121
  AMP PEAK 23(17Q25.3) WILD-TYPE   6 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q25.3) MUTATED      4  121
  AMP PEAK 23(17Q25.3) WILD-TYPE    6  204
                        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                            204
[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    65  70
  AMP PEAK 24(18Q11.2) WILD-TYPE 201 220
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           135                            421 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            70                            220 
$`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-09-0369 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 TCGA-09-2055 TCGA-10-0927 
       35.57        38.43        41.62        55.36        26.93        81.47 
TCGA-10-0930 TCGA-10-0937 TCGA-13-0717 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 
       33.24        15.12        24.59        11.54        32.25        31.04 
TCGA-13-0795 TCGA-13-0807 TCGA-13-0885 TCGA-13-0890 TCGA-13-0900 TCGA-13-0901 
       19.59        13.61        91.40        67.99        57.07        19.36 
TCGA-13-0904 TCGA-13-0919 TCGA-13-0920 TCGA-13-1407 TCGA-13-1410 TCGA-13-1411 
       48.33        14.89        13.81         6.05         4.70         4.21 
TCGA-13-1489 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
       82.88         4.24        54.31        38.40        13.97        16.57 
TCGA-13-1507 TCGA-13-2059 TCGA-13-2060 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 
        4.77        12.23         8.61        27.52        19.10        16.70 
TCGA-23-1024 TCGA-23-1110 TCGA-23-1114 TCGA-23-1123 TCGA-23-1809 TCGA-23-2078 
       15.39        54.51        68.68        33.47         0.53        87.48 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 TCGA-24-0982 TCGA-24-1422 
        4.50         7.63        19.66        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        19.17        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        32.02 
TCGA-25-1315 TCGA-25-1319 TCGA-25-1633 TCGA-25-1635 TCGA-25-1878 TCGA-25-2393 
       51.06        65.00        60.59        51.22        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         0.79        68.32        18.25 
TCGA-29-1761 TCGA-29-1766 TCGA-29-1784 TCGA-29-2425 TCGA-29-2432 TCGA-29-2434 
       17.00        39.12         5.36        65.00        11.84        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 
      125.75         8.61         0.79 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       63.09        48.76        63.98        65.46        49.28        32.52 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1517 
       44.32        33.67        76.57        71.47        56.55        19.99 
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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       45.37        29.16         9.47        57.76        17.98         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 
       89.33        74.93        57.60        61.87        30.51        17.98 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
       35.15         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0931 
       20.94        12.46        54.31        25.91        18.51        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 
       11.70         3.91        35.44        35.80        19.86         6.21 
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        31.10        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 
       17.82        55.17         2.50        11.18        11.38        34.06 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       35.28        35.28        68.94       107.18        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       70.39        61.84        69.01        43.36        57.47        56.15 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       47.38        47.84        44.94        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 
       10.88         6.61         7.36         5.92         6.84         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       22.39        70.82        52.44        73.55        38.20        49.25 
TCGA-13-1498 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 
       37.61        32.84         4.21         4.41         4.18         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
        3.91         3.09        14.24        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 
       54.77         8.42        23.05        25.94        26.20        72.20 
TCGA-20-1683 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       25.38         2.93         2.66        47.54        42.54        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 
        2.24        51.35         3.22        31.20         4.57        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-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
       24.95       115.89        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
        4.70        11.64        21.80         7.66        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-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1463 
        6.25         6.02         5.95         5.36         4.83        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-24-1567 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-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.79         9.80        22.68        16.44        11.05        81.11 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 
       44.84        58.16       109.71        14.43        53.95        18.48 
TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 
       28.18        64.01        44.52        57.07         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 
       31.63        70.45        36.23        16.64        33.11        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 
        1.02        26.96        37.02         1.02        34.98        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       35.54        14.96        24.99        18.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 
        1.02         3.02        45.01        19.99         2.96        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 
       26.99        78.90        44.71        47.18       101.79        38.53 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.70        31.20         0.53        16.90        18.67        59.67 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       41.98        29.23        34.62        85.68        66.81        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       31.23        22.98        24.36        22.55        17.33        12.36 
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        34.62 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 
       86.17        62.47        45.11         4.90        42.25         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       21.04        38.07        51.91         2.47        15.68         0.26 
TCGA-30-1859 TCGA-30-1861 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1891 
       48.10        34.78         1.22        57.57        24.26        30.05 
TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 
       48.79        45.57        30.18        18.77        22.49        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1575 TCGA-36-1576 
       44.12        28.77        29.10        21.53         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       25.74        27.85        24.23        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-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       18.31        14.17         6.05        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        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-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2363 TCGA-59-2372 
       25.02        80.12        22.32        34.39         5.42        44.81 
TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       20.52        11.11        20.94        31.43        18.54         4.34 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
       28.47        48.79        44.84        35.80        33.67        43.69 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
        1.45         5.79        11.41        13.02         9.07        34.13 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 
       37.05        42.51        48.92        56.61        67.76        15.75 
TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2016 
        2.01        14.50        17.98         4.01        39.85         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96        45.40         4.80        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-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       44.52        22.22         6.35        31.07        39.68        18.94 
TCGA-WR-A838 
        8.05 

  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                         129.96 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                         28.37                          27.85 
[1] "0.5 - 180.2 (28.4)" "0.3 - 130.0 (27.9)"
[1] "hr=" "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       2   422                0
D24V3, multiclass
                  clus
vv                 AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     135                            422
  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, continuous
D24V5, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     1 138
  AMP PEAK 24(18Q11.2) WILD-TYPE   2 430
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      1  138
  AMP PEAK 24(18Q11.2) WILD-TYPE    2  430
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  NO                             1                              2
  YES                          138                            430
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 24(18Q11.2) MUTATED    4  6  1  0
  AMP PEAK 24(18Q11.2) WILD-TYPE 10 20  4  3
D24V6, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  R0                            4                             10
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(18Q11.2) MUTATED                                  1     6
  AMP PEAK 24(18Q11.2) WILD-TYPE                                2    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(18Q11.2) MUTATED                           5
  AMP PEAK 24(18Q11.2) WILD-TYPE                        27
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 24(18Q11.2) MUTATED                                           0
  AMP PEAK 24(18Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 24(18Q11.2) MUTATED     118
  AMP PEAK 24(18Q11.2) WILD-TYPE   357
D24V7, multiclass
                                           clus
vv                                          AMP PEAK 24(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              118
                                           clus
vv                                          AMP PEAK 24(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                357
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     4  77
  AMP PEAK 24(18Q11.2) WILD-TYPE   6 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      4   77
  AMP PEAK 24(18Q11.2) WILD-TYPE    6  248
                        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                            248
[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   148 157
  AMP PEAK 25(19P13.12) WILD-TYPE 118 133
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            305                             251 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                            157                             133 
$`AMP PEAK 25(19P13.12) MUTATED`
TCGA-04-1335 TCGA-04-1342 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 
        1.81        18.51        65.52        48.76        21.57        63.98 
TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1514 
       49.28        44.32        33.67        76.57        82.39        56.55 
TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       41.59        19.99        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 
       48.89        27.88        28.64        64.64        31.86        47.70 
TCGA-09-0364 TCGA-09-0367 TCGA-09-1659 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 
       29.16        17.98         9.99        41.62        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       30.51        17.98         3.02         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2053 TCGA-09-2054 TCGA-10-0926 TCGA-10-0927 
        6.12       112.41        39.75        20.94        25.91        81.47 
TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 TCGA-13-0724 TCGA-13-0727 TCGA-13-0751 
       11.70        35.80        19.86         2.73        15.19        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 
       11.18        11.54        34.06        32.25        31.04         8.45 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 
       38.93        30.35        19.59         8.12         8.19        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       35.28        13.61        68.94       107.18        74.27        66.67 
TCGA-13-0888 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0905 
       70.39        69.01        57.47        56.15        19.36        47.84 
TCGA-13-0910 TCGA-13-0912 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 
       37.08        34.06         4.64         6.41        10.88         6.61 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1482 
        6.05         5.92         6.84         4.70        87.06        61.71 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 TCGA-13-1496 
       98.04        22.39        82.88        52.44        49.25         4.24 
TCGA-13-1497 TCGA-13-1504 TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 
       54.31        16.57         4.41         4.18         2.56        14.24 
TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       12.23        10.78         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-23-1024 TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       47.54        15.39        26.83        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
       51.35         3.22         4.57        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-23-2077 TCGA-23-2078 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 
      115.89        87.48         4.70         4.50         7.63        19.66 
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        19.17 
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        32.02        51.06         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       65.00        36.95        33.96         2.99        12.00         2.96 
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        47.18 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 
      101.79         0.79        31.20        68.32         0.53        18.67 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1770 
       59.67        41.98        29.23        34.62        17.00        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        34.62        86.17         4.90 
TCGA-29-2431 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 
       42.25        11.47        21.04        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        26.04        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 
       22.22        39.68        18.94         0.79         8.05 

$`AMP PEAK 25(19P13.12) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00        49.15         2.01        46.62        11.87 
TCGA-04-1347 TCGA-04-1351 TCGA-04-1361 TCGA-04-1367 TCGA-04-1536 TCGA-04-1651 
       63.09        65.46        32.52        71.47        29.10        36.23 
TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 
       45.37         9.47        57.76        35.57        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-10-0925 TCGA-10-0928 TCGA-10-0930 
       63.09        26.93        12.46        54.31        18.51        33.24 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 
       32.28         3.91        35.44        15.12         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        31.10        17.82         2.50 
TCGA-13-0758 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       11.38        21.40        36.72        28.70         8.71         7.79 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0885 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
        8.28        35.28        91.40        61.84        67.99        43.36 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 
       57.07        47.38        48.33        44.94        44.84        27.72 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 TCGA-13-1405 
       29.98        21.17        14.89        13.81         6.08         7.36 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 
        4.21         5.33        54.64        29.42        20.68        70.82 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       73.55        38.20        37.61        38.40        13.97        32.84 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-2065 
        4.21         4.77         3.91         3.09         8.61         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-20-0996 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 
        6.28        54.77        72.20        42.54        40.54        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-2072 
       49.41         8.81        54.51        31.20        68.68        24.95 
TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-24-0975 TCGA-24-0980 
       91.66        77.00        49.84         2.76        21.80         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
       54.12        63.55         7.86         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
        4.83        28.37        18.67        72.92        12.46         9.11 
TCGA-24-1470 TCGA-24-1544 TCGA-24-1546 TCGA-24-1551 TCGA-24-1552 TCGA-24-1560 
        3.45        26.96        64.27        51.91        41.39        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1846 
       45.50        47.70        25.87        17.23        90.15         4.37 
TCGA-24-1849 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 
        5.79        22.68        30.21        16.44        81.11         4.87 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       44.84        58.16        34.82        14.43        53.95        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2288 
       64.01        44.52        57.07         0.36        31.63         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1316 
       67.36        36.23        16.64        55.86        26.96        37.02 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       18.02        15.81         0.36         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 
       60.59        35.54        51.22        24.99        18.05        13.02 
TCGA-25-2391 TCGA-25-2392 TCGA-25-2397 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 
       49.05         1.02        12.00        29.03        31.00        78.90 
TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 TCGA-29-1705 TCGA-29-1762 
       44.71        38.53        33.70        16.90        18.25        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 
       66.81        62.93        39.12        31.23        22.98        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2425 
       17.33        11.84        12.30         8.38         5.36        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2432 TCGA-29-2436 TCGA-30-1718 TCGA-30-1861 
       62.47        45.11        11.84         9.76        51.91        34.78 
TCGA-30-1880 TCGA-30-1891 TCGA-31-1946 TCGA-31-1953 TCGA-31-1956 TCGA-36-1569 
       57.57        30.05        30.18         6.71        44.12        29.10 
TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2532 
       30.08        25.74        27.85        24.23        24.69        29.49 
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-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
       16.18         7.99        23.74         9.44         7.46        40.77 
TCGA-57-1582 TCGA-57-1585 TCGA-57-1992 TCGA-57-1994 TCGA-59-2349 TCGA-59-2354 
       24.03         1.74        29.00        25.02        80.12        34.39 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 TCGA-61-1733 
       44.81        20.52        11.11         8.09        18.54        31.79 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 
       28.47        48.79        44.84         2.43         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1995 
        5.79        11.41        13.02        31.30        37.05         2.01 
TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2092 
        5.52        17.98         4.01        30.64         1.18        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       71.74        61.64         6.35        31.07         8.61 

  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                           91.66 
  AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE 
                          26.83                           29.00 
[1] "0.3 - 180.2 (26.8)" "0.3 - 91.7 (29.0)" 
[1] "hr=" "1.1"
D25V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 25(19P13.12) MUTATED         0   306                1
  AMP PEAK 25(19P13.12) WILD-TYPE       2   251                1
D25V3, multiclass
                  clus
vv                 AMP PEAK 25(19P13.12) MUTATED
  OMENTUM                                      0
  OVARY                                      306
  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, continuous
D25V5, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19P13.12) MUTATED     1 311
  AMP PEAK 25(19P13.12) WILD-TYPE   2 257
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19P13.12) MUTATED      1  311
  AMP PEAK 25(19P13.12) WILD-TYPE    2  257
     clus
vv    AMP PEAK 25(19P13.12) MUTATED AMP PEAK 25(19P13.12) WILD-TYPE
  NO                              1                               2
  YES                           311                             257
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 25(19P13.12) MUTATED    9 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                             9                               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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(19P13.12) MUTATED                                  1    10
  AMP PEAK 25(19P13.12) WILD-TYPE                                2     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(19P13.12) MUTATED                          18
  AMP PEAK 25(19P13.12) WILD-TYPE                        14
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 25(19P13.12) MUTATED                                           1
  AMP PEAK 25(19P13.12) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 25(19P13.12) MUTATED     260
  AMP PEAK 25(19P13.12) WILD-TYPE   215
D25V7, multiclass
                                           clus
vv                                          AMP PEAK 25(19P13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                10
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               260
                                           clus
vv                                          AMP PEAK 25(19P13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        2
  ASIAN                                                                   8
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 215
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(19P13.12) MUTATED     6 181
  AMP PEAK 25(19P13.12) WILD-TYPE   4 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(19P13.12) MUTATED      6  181
  AMP PEAK 25(19P13.12) WILD-TYPE    4  144
                        clus
vv                       AMP PEAK 25(19P13.12) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           181
                        clus
vv                       AMP PEAK 25(19P13.12) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             144
[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   147 164
  AMP PEAK 26(19Q12) WILD-TYPE 119 126
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         311                          245 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                         164                          126 
$`AMP PEAK 26(19Q12) MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       41.00        46.62        18.51        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 
       48.76        21.57        49.28        44.32        33.67        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       56.55        41.59        19.99        38.37       119.08        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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       47.70        29.16         9.47        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
        9.99        38.43        41.62        61.87        55.36        30.51 
TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2050 
       17.98         3.02         8.55        97.55         6.18        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0933 TCGA-10-0936 TCGA-10-0938 
       63.09        39.75        20.94        11.70        35.80        19.86 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       24.59        39.58         2.73        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 
       11.18        11.54        34.06        31.04         8.45        38.93 
TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 
       36.72        30.35        19.59         8.71         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 
       43.86        35.28        13.61        68.94        91.40        74.27 
TCGA-13-0888 TCGA-13-0893 TCGA-13-0904 TCGA-13-0905 TCGA-13-0911 TCGA-13-0920 
       70.39        43.36        48.33        47.84        27.72        13.81 
TCGA-13-0923 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        6.41         6.05         5.92         4.70         4.21        87.06 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       61.71        98.04        22.39        82.88        52.44        73.55 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 
       49.25         4.24        13.97        16.57         4.41         4.77 
TCGA-13-1511 TCGA-13-2060 TCGA-13-2061 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        3.91         8.61        10.78         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-23-1022 TCGA-23-1024 TCGA-23-1030 TCGA-23-1031 
        2.66        47.54        42.54        15.39        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 
        2.24        51.35        54.51         3.22         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2084 TCGA-23-2645 TCGA-24-0966 
        0.53        24.95       115.89        49.84         4.50         7.63 
TCGA-24-0968 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 
       19.66        41.56        22.32        47.41         6.31         7.82 
TCGA-24-1418 TCGA-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        7.99         6.02         5.36        17.39        19.17        18.67 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 
        8.55        45.14       105.99         9.11         1.18        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-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       58.09        39.88        19.53        48.33        38.24         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-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 
       22.68         4.87       152.02        44.84       109.71        53.95 
TCGA-24-2033 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 
       18.48         0.79        47.54        70.45        44.61         0.82 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       33.11        53.26         1.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 
       36.95        33.96        12.00         2.96        18.58        15.81 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 
       20.61         0.30        51.22        24.99        18.05        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-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       47.18        38.53         0.79        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       16.90        59.67        41.98        29.23        34.62        17.00 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 
       66.81        39.12        24.36        17.33        12.36        14.93 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 
        8.38         7.23        34.62        86.17        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       42.25        11.84        11.47        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 
        2.47        15.68        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-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 
        6.71         2.20        28.77        30.08        27.85        24.69 
TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 
       35.05        29.82        25.91         2.24        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2593 
       16.18        11.47        26.04        23.74        42.02         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-59-2350 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
       25.02       180.20        22.32       116.12        34.39         2.14 
TCGA-61-1722 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1740 
        8.09        27.88         4.34        31.79        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 
       33.67        43.69         1.45         8.42         9.07        34.13 
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-61-2000 TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 
       38.17        14.50         4.01        30.64         1.18        45.96 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
        4.80         4.77        58.39        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2111 TCGA-61-2113 TCGA-61-2614 TCGA-WR-A838 
       76.87       125.75        22.22         8.61         8.05 

$`AMP PEAK 26(19Q12) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1350 TCGA-04-1351 
       40.24         1.81        49.15         2.01        63.98        65.46 
TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1648 TCGA-04-1651 TCGA-04-1655 
       32.52        76.57        71.47        28.64        36.23        45.37 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1672 TCGA-09-2044 TCGA-09-2045 
       89.33        74.93        57.60         5.85         6.12        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
        4.54       112.41        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 
       81.47        18.51        33.24        32.28         3.91        35.44 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 
       15.12         6.21        44.55        12.39        31.10         2.50 
TCGA-13-0758 TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 TCGA-13-0799 TCGA-13-0800 
       11.38        32.25        21.40        28.70         7.79         8.12 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       35.28       107.18        66.67        61.84        67.99        69.01 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 
       57.47        56.15        57.07        19.36        47.38        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        34.06        29.98        21.17        14.89 
TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 
        4.64         6.08        10.88         6.61         7.36         6.84 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 TCGA-13-1494 
        5.33        54.64        29.42        20.68        70.82        38.20 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1509 
       54.31        37.61        38.40        32.84         4.21         4.18 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 
        2.56         3.09        14.24        12.23         8.75         6.28 
TCGA-13-A5FT TCGA-20-0996 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       54.77        72.20        40.54        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1113 TCGA-23-1114 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 
        8.81        31.20        68.68        58.13        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 
       77.00         2.76         4.70        11.64        21.80         7.66 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
       54.12        63.55         6.38         7.86         0.76         6.25 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 
        5.95         4.83        28.37        43.53        72.92        12.46 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1546 TCGA-24-1555 TCGA-24-1556 TCGA-24-1560 
        3.45        22.22        64.27        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-24-1846 TCGA-24-1849 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
       88.37         4.37         5.79        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 
       81.11        58.16        34.82        14.43        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 TCGA-24-2271 TCGA-24-2289 
       44.52        57.07        36.16         0.36        31.63        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       36.23        16.64        55.86        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1322 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 TCGA-25-1632 
       37.02         2.99        18.02         0.36         7.86        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       60.59        35.54        14.96        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2400 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
        1.02        42.02        31.00        26.99        78.90        44.71 
TCGA-29-1693 TCGA-29-1696 TCGA-29-1702 TCGA-29-1705 TCGA-29-1762 TCGA-29-1764 
      101.79        33.70        18.67        18.25        85.68        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1784 
       31.23        22.98        22.55        11.84        12.30         5.36 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1857 TCGA-30-1861 
       65.00        62.47         9.76        21.04         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-3P-A9WA TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
       18.31         6.05         7.99         9.44         7.46        40.77 
TCGA-57-1992 TCGA-59-2349 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
       29.00        80.12         9.40         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       11.11        20.94        31.43        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
       44.84         5.79        11.41        13.02        31.30        37.05 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 TCGA-61-2018 
        2.01         5.52        17.98        30.64        39.85        45.40 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 
       51.72        71.74        61.64        55.50        20.68        44.52 
TCGA-61-2612 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        6.35        31.07        39.68        18.94         0.79 

  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                       112.41 
  AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE 
                       25.91                        29.98 
[1] "0.3 - 180.2 (25.9)" "0.3 - 112.4 (30.0)"
[1] "hr=" "1.1"
D26V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 26(19Q12) MUTATED         0   310                2
  AMP PEAK 26(19Q12) WILD-TYPE       2   247                0
D26V3, multiclass
                  clus
vv                 AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  OMENTUM                                   0                            2
  OVARY                                   310                          247
  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, continuous
D26V5, binary
                              cls
clus                             0   1
  AMP PEAK 26(19Q12) MUTATED     2 315
  AMP PEAK 26(19Q12) WILD-TYPE   1 253
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      2  315
  AMP PEAK 26(19Q12) WILD-TYPE    1  253
     clus
vv    AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
  NO                           2                            1
  YES                        315                          253
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 26(19Q12) MUTATED    8 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                          8                            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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(19Q12) MUTATED                                  2     7
  AMP PEAK 26(19Q12) WILD-TYPE                                1    11
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(19Q12) MUTATED                          17
  AMP PEAK 26(19Q12) WILD-TYPE                        15
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 26(19Q12) MUTATED                                           1   271
  AMP PEAK 26(19Q12) WILD-TYPE                                         0   204
D26V7, multiclass
                                           clus
vv                                          AMP PEAK 26(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              7
  BLACK OR AFRICAN AMERICAN                                         17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            271
                                           clus
vv                                          AMP PEAK 26(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                               11
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              204
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                              cls
clus                             0   1
  AMP PEAK 26(19Q12) MUTATED     6 181
  AMP PEAK 26(19Q12) WILD-TYPE   4 144
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(19Q12) MUTATED      6  181
  AMP PEAK 26(19Q12) WILD-TYPE    4  144
                        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                          144
[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   106 130
  AMP PEAK 27(19Q13.2) WILD-TYPE 160 160
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           236                            320 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                           130                            160 
$`AMP PEAK 27(19Q13.2) MUTATED`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 
       41.00        18.51        11.87        65.52        63.09        48.76 
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-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1649 TCGA-04-1652 TCGA-09-0364 
       38.37       119.08        29.10        64.64        31.86        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1665 TCGA-09-1668 TCGA-09-1669 
        9.47        17.98        35.57        41.62        55.36        30.51 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 TCGA-10-0927 
        8.55         6.18         4.54        63.09        39.75        81.47 
TCGA-10-0933 TCGA-13-0717 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       11.70        24.59         2.73        15.19        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0768 TCGA-13-0791 
        2.50        11.18        11.54        34.06         8.45        38.93 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0807 
       30.35        19.59         8.71         8.12         8.19        13.61 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0905 
       68.94        91.40        74.27        70.39        67.99        47.84 
TCGA-13-0916 TCGA-13-0920 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       21.17        13.81         6.05         5.92         4.70         4.21 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 
       61.71        98.04        22.39        73.55        49.25         4.24 
TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-2061 
       13.97        32.84        16.57         4.41         4.77        10.78 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0991 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       54.77        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        42.54        15.39        29.13         2.24        54.51 
TCGA-23-1111 TCGA-23-1116 TCGA-23-1117 TCGA-23-1121 TCGA-23-1809 TCGA-23-2072 
        3.22         4.57        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        19.17        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        53.95        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         1.02        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1635 TCGA-25-1871 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       51.22        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        47.18         0.79        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
        0.53        16.90        18.25        17.00        85.68        66.81 
TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 
       39.12        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 
       34.62        62.47        45.11         4.90        11.84        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        26.04        23.74         9.44        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 
       18.94         8.05 

$`AMP PEAK 27(19Q13.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1349 
       40.24         1.81        49.15         2.01        46.62        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98        65.46        49.28        33.67        76.57        71.47 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1651 
       84.20        55.43        48.89        27.88        28.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       47.70        45.37        57.76         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       74.93        57.60        61.87        17.98         5.85         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 
       97.55         6.12        35.15       112.41        71.11        20.94 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 
       26.93        12.46        54.31        25.91        18.51        33.24 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       32.28         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 
        6.21        44.55        39.58        12.39        31.10        11.38 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0799 
       32.25        31.04        21.40        36.72        28.70         7.79 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0887 
        8.28        43.86        35.28        35.28       107.18        66.67 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       61.84        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        48.33        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       27.72        34.06        29.98        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 
        6.08        10.88         6.61         7.36         6.84         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 
       54.64        87.06        29.42        20.68        70.82        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 
       52.44        38.20        54.31        37.61        38.40         4.21 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0996 
        8.61         8.75         6.28         8.42        25.94        72.20 
TCGA-20-1682 TCGA-20-1683 TCGA-23-1021 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
       27.52        25.38        47.54        40.54        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1113 TCGA-23-1114 
       49.41         8.81        18.90        51.35        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-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        91.66        77.00         2.76         4.70 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 
        7.63        19.66        11.64        21.80         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1413 TCGA-24-1416 TCGA-24-1419 TCGA-24-1422 
       54.12        63.55         6.31         6.38         7.86         0.76 
TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 
        6.25         5.95         4.83        28.37        43.53        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1546 TCGA-24-1551 
       12.46       105.99         3.45        22.22        64.27        51.91 
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-24-1844 
       10.26        17.23        90.15        88.37        38.24         3.72 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        4.37         5.79         9.80        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2035 
       81.11         4.87        58.16        34.82        14.43        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2290 
       64.01        44.52        57.07         0.36        31.63        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        32.02        51.06        37.02 
TCGA-25-1319 TCGA-25-1625 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 
       65.00        18.02        60.59        35.54        14.96        18.05 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2400 TCGA-25-2408 
       85.05        13.02        49.05        38.04        42.02        31.00 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        44.71       101.79        38.53        33.70 
TCGA-29-1698 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 
       68.32        18.67        59.67        41.98        29.23        34.62 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 
       62.93        31.23        22.98        22.55        11.84        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2431 TCGA-29-2434 
        8.38         7.23        86.17        65.00        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1861 
        9.76        21.04        36.26         2.47        15.68        34.78 
TCGA-30-1862 TCGA-30-1880 TCGA-30-1891 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
        6.12        57.57        30.05        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-36-1580 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 
        8.55        25.74        24.23        24.69        33.01        29.49 
TCGA-36-2534 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 
       29.82        25.08        23.80        21.60        18.31        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 
        6.05        16.18         7.99         7.46        40.77        11.38 
TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       21.14        22.32        29.00        80.12        22.32         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1724 
        2.14         5.42        44.81        20.52        11.11        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       31.43        18.54        31.79        28.47        44.84        35.80 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
       43.69         1.45         5.79        13.02        31.30        37.05 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       67.76        43.43        15.75        38.17         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-61-2018 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-61-2101 TCGA-61-2102 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 
       55.50         6.48        20.68        44.52       125.75        31.07 
TCGA-OY-A56P TCGA-VG-A8LO 
       39.68         0.79 

  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                         129.96 
  AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE 
                        23.395                         30.425 
[1] "0.3 - 180.2 (23.4)" "0.4 - 130.0 (30.4)"
[1] "hr=" "1.3"
D27V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 27(19Q13.2) MUTATED         0   236                2
  AMP PEAK 27(19Q13.2) WILD-TYPE       2   321                0
D27V3, multiclass
                  clus
vv                 AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     236                            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, continuous
D27V5, binary
                                cls
clus                               0   1
  AMP PEAK 27(19Q13.2) MUTATED     2 239
  AMP PEAK 27(19Q13.2) WILD-TYPE   1 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(19Q13.2) MUTATED      2  239
  AMP PEAK 27(19Q13.2) WILD-TYPE    1  329
     clus
vv    AMP PEAK 27(19Q13.2) MUTATED AMP PEAK 27(19Q13.2) WILD-TYPE
  NO                             2                              1
  YES                          239                            329
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 27(19Q13.2) MUTATED    5 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                            5                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(19Q13.2) MUTATED                                  2     4
  AMP PEAK 27(19Q13.2) WILD-TYPE                                1    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(19Q13.2) MUTATED                           7
  AMP PEAK 27(19Q13.2) WILD-TYPE                        25
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 27(19Q13.2) MUTATED                                           1
  AMP PEAK 27(19Q13.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  AMP PEAK 27(19Q13.2) MUTATED     210
  AMP PEAK 27(19Q13.2) WILD-TYPE   265
D27V7, multiclass
                                           clus
vv                                          AMP PEAK 27(19Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                4
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              210
                                           clus
vv                                          AMP PEAK 27(19Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                265
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                                cls
clus                               0   1
  AMP PEAK 27(19Q13.2) MUTATED     5 136
  AMP PEAK 27(19Q13.2) WILD-TYPE   5 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(19Q13.2) MUTATED      5  136
  AMP PEAK 27(19Q13.2) WILD-TYPE    5  189
                        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                            189
[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   145 161
  AMP PEAK 28(20P13) WILD-TYPE 121 129
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         306                          250 
  AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE 
                         161                          129 
$`AMP PEAK 28(20P13) MUTATED`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       40.24         2.01        18.51        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       21.57        63.98        49.28        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1542 TCGA-04-1646 
       71.47        56.55        41.59        19.99        84.20        27.88 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 
       64.64        36.23        45.37        57.76        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 
        9.99        38.43        41.62        55.36        17.98         8.55 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 
        6.12       112.41        71.11        63.09        39.75        26.93 
TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       81.47        32.28        11.70        35.44        35.80        19.86 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0751 
       24.59        44.55         2.73        12.39        15.19        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
       11.18        11.38        11.54        34.06        31.04        21.40 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       38.93        30.35         8.12         8.28         8.19        43.86 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0899 TCGA-13-0904 
      107.18        91.40        66.67        70.39        56.15        48.33 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1405 
       29.98        14.89        13.81         6.41         6.08         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 
        6.05         5.92         6.84         4.70        87.06        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1497 
       20.68        22.39        70.82        82.88        73.55        54.31 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 
       38.40        16.57         4.21         4.41         4.77        14.24 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
       12.23        10.78         8.75        54.77         8.42        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-23-1021 TCGA-23-1024 
       26.20        25.38        19.10        16.70        47.54        15.39 
TCGA-23-1026 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 
       26.83        29.13        18.90         2.24        51.35         3.22 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 
       68.68         4.57        86.01         4.27         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53        24.95        87.48        91.66 
TCGA-23-2084 TCGA-23-2643 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 
       49.84         4.70        22.32        47.41         6.31         7.99 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        0.76         6.25         6.02        28.37        19.17        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-24-1548 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1564 
       16.21        51.91        58.09        70.62        39.88        25.87 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1616 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 
       17.23        88.37        38.24         3.48         3.72         3.81 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1930 TCGA-24-2020 
       11.28         5.52         9.80        22.68        81.11       152.02 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2260 TCGA-24-2267 TCGA-24-2280 
       34.82        53.95        18.48        36.16        47.54        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-25-1312 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        26.96        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 
       65.00        36.95        33.96        12.00        18.58        15.81 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        0.36        20.61         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 
       51.22        14.96        24.99        18.05        85.05        38.04 
TCGA-25-2396 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 TCGA-29-1688 TCGA-29-1695 
        3.02        42.02        29.03        31.00        78.90         0.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 
       31.20        68.32         0.53        16.90        59.67        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 
       29.23        34.62        66.81        62.93        39.12        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1783 
       22.98        24.36        12.36        11.84        14.93         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
        5.36        34.62        86.17        65.00        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 
       42.25        11.84        21.04        38.07        51.91         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 TCGA-30-1887 
       15.68         0.26        48.10         6.12         1.22        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       30.05        48.79        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-36-1580 TCGA-36-2530 TCGA-36-2534 TCGA-36-2543 
        8.55        30.08        24.23        33.01        29.82         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       20.98        18.31        20.52        14.17         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 
       11.47         7.99        23.74        42.02         7.46         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 TCGA-57-1994 TCGA-59-2351 
       24.03        11.38         1.74        22.32        25.02       116.12 
TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1730 
        9.40         5.42        44.81        20.52         8.09         4.34 
TCGA-61-1733 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
       31.79        43.69         1.45         8.42         5.79        13.02 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 
        9.07        34.13        37.05        42.51        67.76        15.75 
TCGA-61-1919 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       38.17        17.98         4.01        30.64        39.85        30.64 
TCGA-61-2018 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 
       45.40        60.62        65.52        55.50         6.48        76.87 
TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22         6.35         8.61        39.68        18.94         0.79 

$`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-04-1361 TCGA-04-1371 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       32.52        82.39        38.37       119.08        29.10        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1652 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 
       48.89        28.64        31.86        47.70        29.16         9.47 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 
       89.33        74.93        57.60        61.87        30.51         5.85 
TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2054 
        3.02        97.55         6.18        35.15         4.54        20.94 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0934 
       12.46        54.31        25.91        18.51        33.24         3.91 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0723 TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 
       15.12         6.21        39.58        31.10        17.82         2.50 
TCGA-13-0762 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
       32.25         8.45        36.72        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 
        7.79        35.28        35.28        13.61        68.94        74.27 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       61.84        67.99        69.01        43.36        57.47        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       19.36        47.38        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 TCGA-13-1403 TCGA-13-1404 
       27.72        34.06        21.17         4.64        10.88         6.61 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1491 
        4.21         5.33        54.64        61.71        29.42        52.44 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25         4.24        37.61        13.97        32.84 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2060 TCGA-13-2071 
        4.18         2.56         3.91         3.09         8.61         6.28 
TCGA-20-0987 TCGA-20-0996 TCGA-20-1682 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 
       23.05        72.20        27.52         2.93         2.66        42.54 
TCGA-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1110 TCGA-23-1113 
       40.54        31.76        49.41         8.81        54.51        31.20 
TCGA-23-1117 TCGA-23-1119 TCGA-23-2077 TCGA-23-2081 TCGA-23-2641 TCGA-23-2645 
       33.30       129.96       115.89        77.00         2.76         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        7.63        19.66        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        32.02 
TCGA-25-1322 TCGA-25-1329 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 
        2.99         2.96        18.02         7.86        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 
       44.71        47.18       101.79        38.53        33.70        18.67 
TCGA-29-1705 TCGA-29-1761 TCGA-29-1762 TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 
       18.25        17.00        85.68        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        26.04         9.44        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 
       44.52       125.75        31.07         8.05 

  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 
                      25.005                       30.360 
[1] "0.3 - 152.0 (25.0)" "0.4 - 180.2 (30.4)"
[1] "hr=" "1.1"
D28V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 28(20P13) MUTATED         2   306                1
  AMP PEAK 28(20P13) WILD-TYPE       0   251                1
D28V3, multiclass
                  clus
vv                 AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE
  OMENTUM                                   2                            0
  OVARY                                   306                          251
  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, continuous
D28V5, binary
                              cls
clus                             0   1
  AMP PEAK 28(20P13) MUTATED     2 312
  AMP PEAK 28(20P13) WILD-TYPE   1 256
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(20P13) MUTATED      2  312
  AMP PEAK 28(20P13) WILD-TYPE    1  256
     clus
vv    AMP PEAK 28(20P13) MUTATED AMP PEAK 28(20P13) WILD-TYPE
  NO                           2                            1
  YES                        312                          256
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 28(20P13) MUTATED    9 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                          9                            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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(20P13) MUTATED                                  2     6
  AMP PEAK 28(20P13) WILD-TYPE                                1    12
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(20P13) MUTATED                          21
  AMP PEAK 28(20P13) WILD-TYPE                        11
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 28(20P13) MUTATED                                           1   260
  AMP PEAK 28(20P13) WILD-TYPE                                         0   215
D28V7, multiclass
                                           clus
vv                                          AMP PEAK 28(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   2
  ASIAN                                                              6
  BLACK OR AFRICAN AMERICAN                                         21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            260
                                           clus
vv                                          AMP PEAK 28(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              215
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                              cls
clus                             0   1
  AMP PEAK 28(20P13) MUTATED     4 175
  AMP PEAK 28(20P13) WILD-TYPE   6 150
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 28(20P13) MUTATED      4  175
  AMP PEAK 28(20P13) WILD-TYPE    6  150
                        clus
vv                       AMP PEAK 28(20P13) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        175
                        clus
vv                       AMP PEAK 28(20P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          150
[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   150 182
  AMP PEAK 29(20Q11.21) WILD-TYPE 116 108
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            332                             224 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                            182                             108 
$`AMP PEAK 29(20Q11.21) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       40.24        49.15         2.01        46.62        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-04-1356 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 
       49.28        33.67        82.39        56.55        19.99        38.37 
TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 
      119.08        84.20        27.88        64.64        31.86        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 
       57.76        17.98        35.57         9.99        38.43        41.62 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2053 
       55.36        17.98         8.55         6.18         6.12        39.75 
TCGA-09-2054 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 
       20.94        33.24        11.70        35.44        35.80        19.86 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       24.59        39.58         2.73        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0791 
       11.18        11.38        11.54        32.25        31.04        38.93 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0884 
       30.35        19.59         8.12         8.19        43.86       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        70.39        67.99        69.01 
TCGA-13-0893 TCGA-13-0899 TCGA-13-0901 TCGA-13-0911 TCGA-13-0919 TCGA-13-0920 
       43.36        56.15        19.36        27.72        14.89        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        6.41         6.08        10.88         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 
        4.70        87.06        98.04        20.68        22.39        70.82 
TCGA-13-1489 TCGA-13-1492 TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       82.88        73.55        38.40        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.41         4.77         3.91         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        8.61        10.78         8.75        54.77         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-23-1021 TCGA-23-1022 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
        2.93        47.54        42.54        29.13        18.90         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 
       51.35        54.51         3.22        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-23-2079 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 
       24.95       115.89        91.66        49.84         4.70         4.50 
TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 
        7.63        11.64        21.80        41.56        22.32        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-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        5.36         4.83        17.39        19.17        18.67         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 
       72.92        12.46        45.14         9.11        22.22        26.96 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 
       57.40        16.21        41.06        51.91        41.39        58.09 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1604 TCGA-24-1842 TCGA-24-1843 
       70.62        39.88        19.53        88.37         8.32         3.48 
TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
        3.72         3.81        11.28         5.52         9.80        22.68 
TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        11.05        81.11         4.87       152.02        44.84 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 
       34.82       109.71        53.95        18.48        36.16         0.79 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 
       47.54        70.45        44.61         0.82        16.64        33.11 
TCGA-24-2298 TCGA-25-1312 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
       53.26         1.02        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       15.81         0.36        20.61         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       35.54        51.22        14.96        24.99        18.05        85.05 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-25-2408 
       38.04         3.02        45.01        42.02        29.03        31.00 
TCGA-29-1691 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
       47.18         0.79        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 
       18.67        59.67        18.25        41.98        29.23        17.00 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 
       66.81        39.12        22.98        24.36        17.33        12.36 
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        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       86.17        65.00        45.11         4.90        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        21.04        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        48.10        34.78         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 
       57.57        24.26        48.79        18.77        22.49         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       42.51         2.20        29.10        22.85         8.55        30.08 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2534 TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 
       24.23        24.69        29.82         2.24        20.52        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2593 TCGA-57-1582 
       16.18        11.47        23.74         9.44         1.48        24.03 
TCGA-57-1583 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       11.38         1.74        29.00        25.08        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
      116.12         9.40         2.14        44.81        20.52         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 
       18.94         8.05 

$`AMP PEAK 29(20Q11.21) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       41.00         1.81        32.52        44.32        76.57        71.47 
TCGA-04-1516 TCGA-04-1536 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 
       41.59        29.10        55.43        48.89        28.64        36.23 
TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       47.70        29.16         9.47        89.33        74.93        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 
       61.87        30.51         5.85         3.02        97.55        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 
        4.54       112.41        71.11        63.09        26.93        12.46 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 
       54.31        25.91        81.47        18.51        32.28         3.91 
TCGA-10-0937 TCGA-13-0714 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 
       15.12         6.21        44.55        12.39        31.10         2.50 
TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 
       34.06        21.40         8.45        36.72        28.70         8.71 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 
        7.79         8.28        35.28        35.28        13.61        68.94 
TCGA-13-0889 TCGA-13-0897 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       61.84        57.47        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        44.84        37.08        34.06        29.98        21.17 
TCGA-13-0921 TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 
        4.64         6.61         7.36         4.21         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       61.71        29.42        52.44        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1509 TCGA-13-1510 TCGA-13-2071 
       54.31        37.61        13.97         4.18         2.56         6.28 
TCGA-20-0996 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       72.20         2.66        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1113 TCGA-23-1116 TCGA-23-1120 TCGA-23-2078 
       49.41         8.81        31.20         4.57         4.27        87.48 
TCGA-23-2081 TCGA-23-2641 TCGA-24-0968 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 
       77.00         2.76        19.66         7.66        54.12        63.55 
TCGA-24-1416 TCGA-24-1419 TCGA-24-1425 TCGA-24-1430 TCGA-24-1435 TCGA-24-1467 
        6.38         7.86         5.95        28.37        43.53       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1546 TCGA-24-1549 TCGA-24-1555 TCGA-24-1560 
        3.45         1.18        64.27        56.58        88.50        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-24-1614 TCGA-24-1616 TCGA-24-1846 TCGA-24-1849 TCGA-24-1927 TCGA-24-2024 
       48.33        38.24         4.37         5.79        16.44        58.16 
TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 
       14.43        28.18        64.01        44.52        57.07         0.36 
TCGA-24-2271 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-25-1313 TCGA-25-1314 
       31.63        67.36        36.23        55.86        26.96        32.02 
TCGA-25-1315 TCGA-25-1625 TCGA-25-1630 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       51.06        18.02         7.86        13.02        49.05         1.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 
       12.00        19.99         2.96        26.99        78.90        44.71 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 
      101.79        38.53        33.70        34.62        85.68        62.93 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-2427 TCGA-29-2432 TCGA-30-1857 
       31.23        22.55        11.84        62.47        11.84         0.26 
TCGA-30-1860 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1956 TCGA-36-1568 
       44.91        30.05        45.57        30.18        44.12        28.77 
TCGA-36-1570 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 TCGA-36-2529 TCGA-36-2530 
       21.53        22.55        25.74        27.85        35.05        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-36-2545 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 
       18.31         6.05         7.99        26.04        42.02         7.46 
TCGA-42-2591 TCGA-57-1584 TCGA-57-1586 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
       40.77        21.14        22.32        80.12        22.32        34.39 
TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1737 
        5.42        11.11        20.94        31.43        28.47        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 
       35.80         2.43         1.45        11.41        13.02        31.30 
TCGA-61-1910 TCGA-61-1913 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       37.05        48.92         2.01         5.52        14.50        17.98 
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-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       71.74        61.64        58.39        20.68        44.52       125.75 
TCGA-61-2613 TCGA-VG-A8LO 
       31.07         0.79 

  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                          125.75 
  AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE 
                         24.475                          30.575 
[1] "0.3 - 180.2 (24.5)" "0.3 - 125.8 (30.6)"
[1] "hr=" "1.2"
D29V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 29(20Q11.21) MUTATED         1   334                1
  AMP PEAK 29(20Q11.21) WILD-TYPE       1   223                1
D29V3, multiclass
                  clus
vv                 AMP PEAK 29(20Q11.21) MUTATED
  OMENTUM                                      1
  OVARY                                      334
  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, continuous
D29V5, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20Q11.21) MUTATED     2 340
  AMP PEAK 29(20Q11.21) WILD-TYPE   1 228
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20Q11.21) MUTATED      2  340
  AMP PEAK 29(20Q11.21) WILD-TYPE    1  228
     clus
vv    AMP PEAK 29(20Q11.21) MUTATED AMP PEAK 29(20Q11.21) WILD-TYPE
  NO                              2                               1
  YES                           340                             228
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 29(20Q11.21) MUTATED    7 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                             7                               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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(20Q11.21) MUTATED                                  2     7
  AMP PEAK 29(20Q11.21) WILD-TYPE                                1    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(20Q11.21) MUTATED                          20
  AMP PEAK 29(20Q11.21) WILD-TYPE                        12
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 29(20Q11.21) MUTATED                                           1
  AMP PEAK 29(20Q11.21) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 29(20Q11.21) MUTATED     289
  AMP PEAK 29(20Q11.21) WILD-TYPE   186
D29V7, multiclass
                                           clus
vv                                          AMP PEAK 29(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               289
                                           clus
vv                                          AMP PEAK 29(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        1
  ASIAN                                                                  11
  BLACK OR AFRICAN AMERICAN                                              12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 186
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                                 cls
clus                                0   1
  AMP PEAK 29(20Q11.21) MUTATED     5 188
  AMP PEAK 29(20Q11.21) WILD-TYPE   5 137
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(20Q11.21) MUTATED      5  188
  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                           188
                        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   183 205
  AMP PEAK 30(20Q13.33) WILD-TYPE  83  85
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            388                             168 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                            205                              85 
$`AMP PEAK 30(20Q13.33) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       40.24        41.00         2.01        46.62        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-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       49.28        44.32        33.67        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1646 TCGA-04-1648 
       19.99        38.37       119.08        29.10        27.88        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       17.98        35.57         9.99        38.43        89.33        41.62 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 
       55.36        30.51        17.98         3.02         8.55         6.18 
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-10-0925 TCGA-10-0928 TCGA-10-0933 TCGA-10-0935 TCGA-10-0936 
       26.93        54.31        18.51        11.70        35.44        35.80 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        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-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        34.06        32.25        21.40         8.45        38.93 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 
       28.70        30.35        19.59         8.12         8.19        43.86 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.28       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 
       67.99        43.36        57.47        56.15        19.36        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 
       47.84        44.94        37.08        27.72        29.98        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 
       13.81         4.64         6.41         6.08        10.88         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
        5.92         6.84         4.70         5.33        87.06        61.71 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 
       98.04        20.68        22.39        82.88        73.55        49.25 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 
        4.41         4.77         4.18         3.91        14.24         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
       10.78         8.75        54.77         8.42        23.05        25.94 
TCGA-20-0991 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       26.20        25.38        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       42.54        15.39        49.41        18.90         2.24        51.35 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 
       54.51         3.22        68.68         4.57        33.30       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-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 
       91.66        77.00        49.84         4.70         4.50         7.63 
TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 
       19.66        21.80        41.56        22.32        47.41         6.31 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.99         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 
        4.83        17.39        19.17        18.67         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 
       12.46        45.14         9.11        22.22        26.96        57.40 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 
       64.27        16.21        58.09        70.62        39.88        19.53 
TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       17.23        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.48         3.72         3.81        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 
        9.80        30.21        11.05         4.87       152.02        58.16 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2254 TCGA-24-2260 
       34.82       109.71        14.43        18.48        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.79         0.36        70.45        44.61         0.82        67.36 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       36.23        16.64        33.11        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       32.02        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 
       33.96        12.00         2.96        18.58        15.81         0.36 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61         0.30        56.94        60.59        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 
       14.96        24.99        18.05        85.05        13.02         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2401 
       38.04         3.02        12.00        45.01        42.02         2.96 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 
       29.03        31.00        26.99        78.90        47.18       101.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.70        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       59.67        18.25        41.98        29.23        34.62        17.00 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 
       66.81        39.12        22.98        24.36        17.33        14.93 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
        7.23         5.36        86.17        65.00        45.11         4.90 
TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        11.47         9.76        21.04        38.07        51.91 
TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       36.26         2.47        15.68        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
        6.12        36.62         1.22        24.26        48.79        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1575 
       18.77        22.49        42.51         2.20        29.10         8.55 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 
       30.08        27.85        24.23        24.69        35.05        29.82 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        9.44        42.02        40.77         1.48        24.03        11.38 
TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 
       22.32        29.00        25.08        25.02       180.20       116.12 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
        9.40         2.14         5.42        44.81        20.52         8.09 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 
       20.94        18.54        27.88         4.34        31.79        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-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
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-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
       38.17        14.50         4.01        30.64        39.85        30.64 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
        4.77        71.74        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
        6.48        76.87        20.68       125.75        22.22         6.35 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        8.61        39.68        18.94         8.05 

$`AMP PEAK 30(20Q13.33) WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 TCGA-04-1542 
        1.81        49.15        32.52        76.57        71.47        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1654 TCGA-09-0365 TCGA-09-1664 TCGA-09-1666 
       55.43        48.89        47.70         9.47        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-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0937 
       25.91        81.47        33.24        32.28         3.91        15.12 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0764 TCGA-13-0792 TCGA-13-0797 TCGA-13-0799 
       31.10         2.50        31.04        36.72         8.71         7.79 
TCGA-13-0801 TCGA-13-0804 TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 TCGA-13-0891 
        8.28        35.28        13.61        68.94        61.84        69.01 
TCGA-13-0900 TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0916 TCGA-13-1404 
       57.07        48.33        44.84        34.06        21.17         6.61 
TCGA-13-1405 TCGA-13-1411 TCGA-13-1477 TCGA-13-1483 TCGA-13-1488 TCGA-13-1491 
        7.36         4.21        54.64        29.42        70.82        52.44 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
       38.20         4.24        54.31         2.56         3.09        12.23 
TCGA-13-2071 TCGA-20-0996 TCGA-20-1682 TCGA-20-1684 TCGA-23-1023 TCGA-23-1026 
        6.28        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 
       31.76         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 
       53.95        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        51.06         2.99        18.02         7.86        49.05 
TCGA-25-2399 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1762 TCGA-29-1764 
       19.99        44.71        38.53         0.79        85.68        62.93 
TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       31.23        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 
       34.62        62.47        11.84         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        26.04 
TCGA-42-2587 TCGA-42-2590 TCGA-57-1584 TCGA-57-1585 TCGA-59-2349 TCGA-59-2350 
       23.74         7.46        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 

  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                          115.89 
  AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE 
                         26.945                          29.770 
[1] "0.3 - 180.2 (26.9)" "0.3 - 115.9 (29.8)"
[1] "hr=" "1.1"
D30V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 30(20Q13.33) MUTATED         2   388                2
  AMP PEAK 30(20Q13.33) WILD-TYPE       0   169                0
D30V3, multiclass
                  clus
vv                 AMP PEAK 30(20Q13.33) MUTATED
  OMENTUM                                      2
  OVARY                                      388
  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, continuous
D30V5, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED     2 395
  AMP PEAK 30(20Q13.33) WILD-TYPE   1 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED      2  395
  AMP PEAK 30(20Q13.33) WILD-TYPE    1  173
     clus
vv    AMP PEAK 30(20Q13.33) MUTATED AMP PEAK 30(20Q13.33) WILD-TYPE
  NO                              2                               1
  YES                           395                             173
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 30(20Q13.33) MUTATED   11 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                            11                               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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 30(20Q13.33) MUTATED                                  3     8
  AMP PEAK 30(20Q13.33) WILD-TYPE                                0    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(20Q13.33) MUTATED                          25
  AMP PEAK 30(20Q13.33) WILD-TYPE                         7
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 30(20Q13.33) MUTATED                                           1
  AMP PEAK 30(20Q13.33) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  AMP PEAK 30(20Q13.33) MUTATED     337
  AMP PEAK 30(20Q13.33) WILD-TYPE   138
D30V7, multiclass
                                           clus
vv                                          AMP PEAK 30(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                            25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               337
                                           clus
vv                                          AMP PEAK 30(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        0
  ASIAN                                                                  10
  BLACK OR AFRICAN AMERICAN                                               7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 138
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                                 cls
clus                                0   1
  AMP PEAK 30(20Q13.33) MUTATED     8 232
  AMP PEAK 30(20Q13.33) WILD-TYPE   2  93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 30(20Q13.33) MUTATED      8  232
  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                           232
                        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    43  46
  AMP PEAK 31(22Q12.2) WILD-TYPE 223 244
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            89                            467 
  AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE 
                            46                            244 
$`AMP PEAK 31(22Q12.2) MUTATED`
TCGA-04-1348 TCGA-04-1356 TCGA-04-1364 TCGA-04-1517 TCGA-04-1536 TCGA-04-1648 
       48.76        49.28        33.67        19.99        29.10        28.64 
TCGA-04-1649 TCGA-04-1654 TCGA-09-1661 TCGA-09-1665 TCGA-09-1667 TCGA-09-1675 
       64.64        47.70        38.43        41.62        61.87        97.55 
TCGA-10-0930 TCGA-10-0936 TCGA-13-0724 TCGA-13-0762 TCGA-13-0794 TCGA-13-0795 
       33.24        35.80         2.73        32.25        30.35        19.59 
TCGA-13-0883 TCGA-13-0888 TCGA-13-0901 TCGA-13-1403 TCGA-13-1405 TCGA-13-1482 
       68.94        70.39        19.36        10.88         7.36        61.71 
TCGA-13-1488 TCGA-13-1495 TCGA-13-1497 TCGA-13-1504 TCGA-13-1511 TCGA-13-2061 
       70.82        49.25        54.31        16.57         3.91        10.78 
TCGA-20-1685 TCGA-20-1686 TCGA-23-1031 TCGA-23-1119 TCGA-23-1122 TCGA-23-2072 
       16.70         2.93        18.90       129.96        39.09        24.95 
TCGA-23-2077 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1469 TCGA-24-1556 
      115.89        17.39        43.53        72.92         9.11        70.62 
TCGA-24-1842 TCGA-24-1845 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 
        8.32         3.81        30.21        16.44        11.05         4.87 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 TCGA-24-2295 
       34.82        53.95        70.45        44.61        36.23        33.11 
TCGA-25-1329 TCGA-25-1627 TCGA-25-1878 TCGA-25-2398 TCGA-29-1699 TCGA-29-1701 
        2.96         0.36        85.05        45.01         0.53        16.90 
TCGA-29-1702 TCGA-29-1764 TCGA-29-1768 TCGA-29-1770 TCGA-29-1777 TCGA-29-1778 
       18.67        62.93        31.23        24.36        12.30        14.93 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-A5NZ TCGA-30-1857 
       65.00        62.47         4.90        42.25        21.04         0.26 
TCGA-30-1861 TCGA-31-1950 TCGA-36-2534 TCGA-36-2547 TCGA-3P-A9WA TCGA-57-1583 
       34.78        18.77        29.82        20.52         7.99        11.38 
TCGA-57-1585 TCGA-61-1727 TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1904 
        1.74        18.54        35.80         2.43        43.69         9.07 
TCGA-61-1911 TCGA-61-2000 TCGA-61-2101 TCGA-61-2111 TCGA-61-2113 
       42.51        14.50        55.50       125.75        22.22 

$`AMP PEAK 31(22Q12.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
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-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       65.46        32.52        44.32        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       48.89        27.88        36.23        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 
        9.47        57.76        17.98        35.57         9.99        89.33 
TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       74.93        57.60        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 
        3.02         8.55         6.18         6.12        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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       12.46        54.31        25.91        81.47        18.51        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       11.70         3.91        35.44        15.12        19.86         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        31.10        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 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       28.70         8.71         7.79         8.12         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.28        13.61       107.18        91.40 
TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        66.67        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       21.17        14.89        13.81         4.64         6.41         6.08 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        87.06        29.42        98.04        20.68 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 
       22.39        82.88        52.44        73.55        38.20         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        13.97        32.84         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.77         4.18         2.56         3.09        14.24        12.23 
TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        8.61         8.75         6.28        54.77         8.42        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        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 
       31.76        49.41         8.81        29.13         2.24        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         4.57        33.30 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 
       86.01         4.27         6.38        33.47        58.13         0.53 
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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 
        4.50         7.63        19.66        11.64        21.80        41.56 
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-24-1418 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-24-1430 TCGA-24-1431 
        6.02         5.95         5.36         4.83        28.37        19.17 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 
       18.67         8.55        12.46        45.14       105.99         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-24-1553 TCGA-24-1555 
       56.58        41.06        51.91        41.39        58.09        88.50 
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-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       10.26        17.23        90.15        88.37        48.33        38.24 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.48         3.72         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 
        9.80        22.68        81.11       152.02        44.84        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        14.43        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       57.07        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2288 TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.82        67.36        16.64        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       65.00        36.95        33.96         2.99        12.00        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       18.02        15.81        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       19.99        42.02         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        44.71        47.18       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       33.70        31.20        68.32        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1766 
       29.23        34.62        17.00        85.68        66.81        39.12 
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-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2432 
        7.23         5.36        34.62        86.17        45.11        11.84 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       11.47         9.76        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        48.10        44.91         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-31-1951 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-36-1569 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-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       25.74        27.85        24.23        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.49        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 
       20.98        18.31        14.17         6.05        16.18        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        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-59-2348 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-59-A5PD TCGA-61-1721 
       34.39         2.14         5.42        44.81        20.52        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-61-1734 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-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        5.79        11.41        13.02        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-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        2.01         5.52        17.98         4.01        30.64        39.85 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
       30.64         1.18        45.96        45.40         4.80         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       51.72        71.74        61.64        58.39        60.62        65.52 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 
        6.48        76.87        20.68        44.52         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68        18.94         0.79         8.05 

  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 
                         30.21                          27.72 
[1] "0.3 - 130.0 (30.2)" "0.3 - 180.2 (27.7)"
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 31(22Q12.2) MUTATED         1    90                0
  AMP PEAK 31(22Q12.2) WILD-TYPE       1   467                2
D31V3, multiclass
                  clus
vv                 AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                      90                            467
  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, continuous
D31V5, binary
                                cls
clus                               0   1
  AMP PEAK 31(22Q12.2) MUTATED     0  91
  AMP PEAK 31(22Q12.2) WILD-TYPE   3 477
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(22Q12.2) MUTATED      0   91
  AMP PEAK 31(22Q12.2) WILD-TYPE    3  477
     clus
vv    AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE
  NO                             0                              3
  YES                           91                            477
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 31(22Q12.2) MUTATED    2  4  0  1
  AMP PEAK 31(22Q12.2) WILD-TYPE 12 22  5  2
D31V6, multiclass
    clus
vv   AMP PEAK 31(22Q12.2) MUTATED AMP PEAK 31(22Q12.2) WILD-TYPE
  R0                            2                             12
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 31(22Q12.2) MUTATED                                  0     2
  AMP PEAK 31(22Q12.2) WILD-TYPE                                3    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(22Q12.2) MUTATED                           5
  AMP PEAK 31(22Q12.2) WILD-TYPE                        27
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 31(22Q12.2) MUTATED                                           0
  AMP PEAK 31(22Q12.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 31(22Q12.2) MUTATED      79
  AMP PEAK 31(22Q12.2) WILD-TYPE   396
D31V7, multiclass
                                           clus
vv                                          AMP PEAK 31(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               79
                                           clus
vv                                          AMP PEAK 31(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                396
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                                cls
clus                               0   1
  AMP PEAK 31(22Q12.2) MUTATED     3  46
  AMP PEAK 31(22Q12.2) WILD-TYPE   7 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 31(22Q12.2) MUTATED      3   46
  AMP PEAK 31(22Q12.2) WILD-TYPE    7  279
                        clus
vv                       AMP PEAK 31(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       AMP PEAK 31(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            279
[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    72  83
  AMP PEAK 32(XP11.23) WILD-TYPE 194 207
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                           155                            401 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                            83                            207 
$`AMP PEAK 32(XP11.23) MUTATED`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
       41.00        18.51        11.87        63.09        21.57        65.46 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1530 TCGA-04-1652 TCGA-09-1661 
       32.52        44.32        33.67       119.08        31.86        38.43 
TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-10-0928 TCGA-10-0933 TCGA-10-0935 
        8.55        35.15         4.54        18.51        11.70        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 TCGA-13-0723 TCGA-13-0726 TCGA-13-0727 
       35.80        15.12        24.59        39.58        31.10        15.19 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0795 
       55.17        11.18         8.45        38.93        28.70        19.59 
TCGA-13-0800 TCGA-13-0807 TCGA-13-0884 TCGA-13-0887 TCGA-13-0890 TCGA-13-0897 
        8.12        13.61       107.18        66.67        67.99        57.47 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-1405 
       19.36        48.33        21.17        13.81         6.41         7.36 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1485 TCGA-13-1488 TCGA-13-1496 TCGA-13-1497 
        5.92         4.70        20.68        70.82         4.24        54.31 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 TCGA-13-2059 
       16.57         4.21         4.41         4.77        14.24        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0991 TCGA-20-1686 TCGA-23-1022 
        8.61         6.28         8.42        26.20         2.93        42.54 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 
       18.90         2.24        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        53.95        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        51.06 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1633 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       65.00        36.95        60.59        14.96        24.99        18.05 
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         0.53        59.67 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1775 
       17.00        66.81        62.93        39.12        31.23        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        21.04         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-59-A5PD TCGA-61-1722 TCGA-61-1911 TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 
       20.52         8.09        42.51        43.43        38.17         2.01 
TCGA-61-2003 TCGA-61-2098 TCGA-61-2109 TCGA-61-2113 TCGA-VG-A8LO 
        4.01        65.52        20.68        22.22         0.79 

$`AMP PEAK 32(XP11.23) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 
       40.24         1.81        49.15         2.01        46.62        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       48.76        63.98        49.28        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        19.99        38.37        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        89.33        74.93        41.62        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-09-2049 TCGA-09-2050 TCGA-09-2051 
       97.55         6.18         6.12       112.41        71.11        63.09 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       39.75        20.94        26.93        12.46        54.31        25.91 
TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-10-0938 TCGA-13-0714 
       81.47        33.24        32.28         3.91        19.86         6.21 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 TCGA-13-0755 TCGA-13-0758 
       44.55         2.73        12.39        17.82         2.50        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 
       11.54        34.06        32.25        31.04        21.40        36.72 
TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       30.35         8.71         7.79         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.28        35.28        68.94        91.40        74.27        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 
       61.84        69.01        43.36        56.15        57.07        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       29.98        14.89         4.64         6.08        10.88         6.61 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.05         6.84         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42        98.04        22.39        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       73.55        38.20        49.25        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 
       32.84         4.18         2.56         3.91         3.09        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1682 
        8.75        54.77        23.05        25.94        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 
       25.38        19.10        16.70         2.66        47.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1109 TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       51.35        31.20         4.57        86.01       129.96        39.09 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
       24.95        87.48        91.66        77.00         2.76         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        19.66        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-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1425 
        7.82         7.99         7.86         0.76         6.02         5.95 
TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 
        5.36        28.37        19.17        18.67        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       72.92        12.46       105.99         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 
       57.40        64.27        16.21        41.06        51.91        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       58.09        88.50        39.88        19.53        44.09        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1845 
       47.70        10.26        17.23        90.15        38.24         3.81 
TCGA-24-1849 TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.79         9.80        22.68        16.44        11.05        81.11 
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-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 
       18.48        28.18        64.01        57.07         0.36        47.54 
TCGA-24-2271 TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 
       31.63         0.82        16.64        33.11        55.86        53.26 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
        1.02        26.96        32.02        37.02         1.02        34.98 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       33.96         2.99        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       35.54        51.22        85.05        13.02        49.05         1.02 
TCGA-25-2393 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       38.04        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        44.71        47.18       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 
       33.70        31.20        68.32        16.90        18.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1769 TCGA-29-1770 
       41.98        29.23        34.62        85.68        22.98        24.36 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1777 TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 
       22.55        17.33        12.30        14.93         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       42.25        11.84         9.76        38.07        51.91        36.26 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1880 TCGA-30-1887 
        0.26        48.10        34.78        36.62        57.57        24.26 
TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1955 
       30.05        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-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 
       22.55         8.55        30.08        25.74        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-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA 
       20.98        18.31        14.17         6.05        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       26.04        23.74         9.44         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2349 
       24.03        11.38        21.14        22.32        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-61-1724 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-61-1736 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-61-1895 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-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        31.30        37.05        48.92        56.61 
TCGA-61-1915 TCGA-61-1918 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 
       67.76        15.75         5.52        14.50        17.98        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-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 
       55.50         6.48        76.87        44.52       125.75         6.35 
TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
       31.07         8.61        39.68        18.94         8.05 

  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                         152.02 
  AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE 
                         21.17                          29.23 
[1] "0.5 - 180.2 (21.2)" "0.3 - 152.0 (29.2)"
[1] "hr=" "1.2"
D32V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 32(XP11.23) MUTATED         1   154                2
  AMP PEAK 32(XP11.23) WILD-TYPE       1   403                0
D32V3, multiclass
                  clus
vv                 AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     154                            403
  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, continuous
D32V5, binary
                                cls
clus                               0   1
  AMP PEAK 32(XP11.23) MUTATED     0 158
  AMP PEAK 32(XP11.23) WILD-TYPE   3 410
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(XP11.23) MUTATED      0  158
  AMP PEAK 32(XP11.23) WILD-TYPE    3  410
     clus
vv    AMP PEAK 32(XP11.23) MUTATED AMP PEAK 32(XP11.23) WILD-TYPE
  NO                             0                              3
  YES                          158                            410
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 32(XP11.23) MUTATED    5  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                            5                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 32(XP11.23) MUTATED                                  0     5
  AMP PEAK 32(XP11.23) WILD-TYPE                                3    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(XP11.23) MUTATED                           8
  AMP PEAK 32(XP11.23) WILD-TYPE                        24
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 32(XP11.23) MUTATED                                           0
  AMP PEAK 32(XP11.23) WILD-TYPE                                         1
                                vv
clus                             WHITE
  AMP PEAK 32(XP11.23) MUTATED     134
  AMP PEAK 32(XP11.23) WILD-TYPE   341
D32V7, multiclass
                                           clus
vv                                          AMP PEAK 32(XP11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              134
                                           clus
vv                                          AMP PEAK 32(XP11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                341
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                                cls
clus                               0   1
  AMP PEAK 32(XP11.23) MUTATED     3  93
  AMP PEAK 32(XP11.23) WILD-TYPE   7 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(XP11.23) MUTATED      3   93
  AMP PEAK 32(XP11.23) WILD-TYPE    7  232
                        clus
vv                       AMP PEAK 32(XP11.23) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       AMP PEAK 32(XP11.23) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            232
[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   104 108
  AMP PEAK 33(XQ28) WILD-TYPE 162 182
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        212                         344 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                        108                         182 
$`AMP PEAK 33(XQ28) MUTATED`
TCGA-04-1335 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1351 TCGA-04-1356 
        1.81        18.51        11.87        65.52        65.46        49.28 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       32.52        33.67        71.47        38.37       119.08        29.10 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0367 TCGA-09-1659 TCGA-09-1666 TCGA-09-1669 
       31.86        45.37        17.98         9.99        57.60        30.51 
TCGA-09-2043 TCGA-09-2049 TCGA-09-2051 TCGA-09-2056 TCGA-10-0927 TCGA-10-0931 
        6.18       112.41        63.09        12.46        81.47        32.28 
TCGA-10-0933 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       11.70        35.80         6.21        24.59        44.55        39.58 
TCGA-13-0725 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 
       12.39        15.19         2.50        11.18        11.54        34.06 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       32.25        21.40        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0888 
        7.79         8.12        13.61        68.94        91.40        70.39 
TCGA-13-0889 TCGA-13-0903 TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0921 
       61.84        47.38        48.33        44.84        34.06         4.64 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
        6.08         6.61         6.84         5.33        87.06        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 TCGA-13-1495 
       29.42        20.68        22.39        70.82        38.20        49.25 
TCGA-13-1496 TCGA-13-1504 TCGA-13-1505 TCGA-13-1511 TCGA-13-2057 TCGA-13-2065 
        4.24        16.57         4.21         3.91        14.24         8.75 
TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 
       23.05        26.20        27.52        25.38        16.70         2.93 
TCGA-20-1687 TCGA-23-1022 TCGA-23-1027 TCGA-23-1028 TCGA-23-1031 TCGA-23-1109 
        2.66        42.54        31.76        49.41        18.90        51.35 
TCGA-23-1111 TCGA-23-1120 TCGA-23-1809 TCGA-23-2079 TCGA-23-2081 TCGA-24-0979 
        3.22         4.27         0.53        91.66        77.00        41.56 
TCGA-24-0980 TCGA-24-1104 TCGA-24-1417 TCGA-24-1419 TCGA-24-1435 TCGA-24-1474 
        7.66        63.55         7.82         7.86        43.53        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-24-1563 TCGA-24-1564 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1846 
       47.70        25.87        38.24         8.32         3.81         4.37 
TCGA-24-1847 TCGA-24-1930 TCGA-24-2020 TCGA-24-2033 TCGA-24-2038 TCGA-24-2261 
       11.28        81.11       152.02        18.48        44.52         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2297 
        0.36        47.54        44.61         0.82        67.36        55.86 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1329 TCGA-25-1625 TCGA-25-1632 TCGA-25-1870 
       26.96        32.02         2.96        18.02        56.94        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 
       24.99        18.05        85.05        13.02         1.02        38.04 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-29-1696 TCGA-29-1701 
        3.02        12.00        45.01        42.02        33.70        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1763 
       18.67        59.67        41.98        29.23        85.68        66.81 
TCGA-29-1764 TCGA-29-1770 TCGA-29-1777 TCGA-29-1778 TCGA-29-1784 TCGA-29-2414 
       62.93        24.36        12.30        14.93         5.36        86.17 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1857 
       11.84        11.47        21.04        38.07        51.91         0.26 
TCGA-30-1862 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
        6.12        24.26        30.05        45.57        30.18        18.77 
TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1575 
       22.49        42.51        44.12        28.77        29.10         8.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2538 TCGA-36-2542 
       25.74        27.85        24.69        35.05        25.08        21.60 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 
       20.98        18.31         6.05        26.04        23.74         9.44 
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-59-2354 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 
       34.39        44.81        20.52         8.09        31.43         4.34 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80         2.43        43.69         1.45         8.42         5.79 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-2002 TCGA-61-2008 TCGA-61-2009 
       42.51        67.76        43.43        17.98        30.64        39.85 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2101 TCGA-61-2104 TCGA-61-2111 
       30.64        45.40         4.77        55.50        76.87       125.75 
TCGA-61-2612 TCGA-61-2614 
        6.35         8.61 

$`AMP PEAK 33(XQ28) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1347 
       40.24        41.00        49.15         2.01        46.62        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1362 TCGA-04-1365 TCGA-04-1371 
       48.76        21.57        63.98        44.32        76.57        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       56.55        41.59        19.99        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 
       27.88        28.64        64.64        36.23        47.70        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
        9.47        57.76        35.57        38.43        89.33        74.93 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 
       41.62        61.87        55.36        17.98         5.85         3.02 
TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2048 TCGA-09-2050 
        8.55        97.55         6.12        35.15         4.54        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 TCGA-10-0928 
       39.75        20.94        26.93        54.31        25.91        18.51 
TCGA-10-0930 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0724 
       33.24         3.91        35.44        15.12        19.86         2.73 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0758 TCGA-13-0764 TCGA-13-0768 
       31.10        17.82        55.17        11.38        31.04         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       38.93        36.72         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 
       35.28       107.18        74.27        66.67        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0905 
       43.36        57.47        56.15        57.07        19.36        47.84 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.94        37.08        27.72        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       13.81         6.41        10.88         7.36         6.05         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1484 TCGA-13-1489 TCGA-13-1491 
        4.70         4.21        54.64        98.04        82.88        52.44 
TCGA-13-1492 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 
       73.55        54.31        37.61        38.40        13.97        32.84 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
        4.41         4.77         4.18         2.56         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 
        8.61        10.78         6.28        54.77         8.42        25.94 
TCGA-20-0996 TCGA-20-1684 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       72.20        19.10        47.54        40.54        15.39        26.83 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 
        8.81        29.13         2.24        54.51        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 
        4.57        33.30        86.01       129.96         6.38        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2084 
       33.47        58.13        24.95       115.89        87.48        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        11.64 
TCGA-24-0975 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 
       21.80        22.32        54.12        47.41         6.31         6.38 
TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 
        7.99         0.76         6.25         6.02         5.95         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 
        4.83        17.39        28.37        19.17        18.67         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-24-1548 TCGA-24-1549 TCGA-24-1550 
        1.18        26.96        57.40        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1565 TCGA-24-1567 
       51.91        19.53        44.09        45.50        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1843 TCGA-24-1844 TCGA-24-1849 
       90.15        88.37        48.33         3.48         3.72         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-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        4.87        44.84        58.16        34.82       109.71        14.43 
TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2271 
       53.95        28.18        64.01        57.07        36.16        31.63 
TCGA-24-2280 TCGA-24-2290 TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 
       70.45        36.23        16.64        33.11        53.26         1.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 
       33.96         2.99        12.00        18.58        15.81         0.36 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 
       20.61         7.86         0.30        60.59        35.54        51.22 
TCGA-25-2391 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 
       49.05        19.99         2.96        29.03        31.00        26.99 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       78.90        44.71        47.18       101.79        38.53         0.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 
       31.20        68.32         0.53        18.25        34.62        17.00 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 
       39.12        31.23        22.98        22.55        17.33        12.36 
TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 
       11.84         8.38         7.23        34.62        65.00        62.47 
TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-30-1853 TCGA-30-1855 
       45.11         4.90        42.25         9.76        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 
       15.68        48.10        44.91        34.78        36.62         1.22 
TCGA-30-1880 TCGA-30-1892 TCGA-31-1953 TCGA-31-1959 TCGA-36-1570 TCGA-36-1571 
       57.57        48.79         6.71         2.20        21.53        22.85 
TCGA-36-1574 TCGA-36-1576 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       22.55        30.08        24.23        33.01        29.49        29.82 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
       25.91        23.80         2.24        20.52        14.17        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       11.47         7.99        42.02         7.46        40.77         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1992 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 
       24.03        11.38        29.00        25.08        80.12        22.32 
TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1724 TCGA-61-1727 
        9.40         2.14         5.42        11.11        20.94        18.54 
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-61-1901 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-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        15.75        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       14.50         4.01         1.18        45.96         4.80        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-61-2113 TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q 
       20.68        44.52        22.22        31.07        39.68        18.94 
TCGA-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  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                      129.96 
  AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE 
                     26.580                      28.555 
[1] "0.3 - 180.2 (26.6)" "0.3 - 130.0 (28.6)"
[1] "hr=" "1.1"
D33V2, continuous
                             vv
clus                          OMENTUM OVARY PERITONEUM OVARY
  AMP PEAK 33(XQ28) MUTATED         0   212                1
  AMP PEAK 33(XQ28) WILD-TYPE       2   345                1
D33V3, multiclass
                  clus
vv                 AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  OMENTUM                                  0                           2
  OVARY                                  212                         345
  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, continuous
D33V5, binary
                             cls
clus                            0   1
  AMP PEAK 33(XQ28) MUTATED     3 213
  AMP PEAK 33(XQ28) WILD-TYPE   0 355
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 33(XQ28) MUTATED      3  213
  AMP PEAK 33(XQ28) WILD-TYPE    0  355
     clus
vv    AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  NO                          3                           0
  YES                       213                         355
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK 33(XQ28) MUTATED    5 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                         5                           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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 33(XQ28) MUTATED                                  1     6
  AMP PEAK 33(XQ28) WILD-TYPE                                2    12
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(XQ28) MUTATED                          11
  AMP PEAK 33(XQ28) WILD-TYPE                        21
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(XQ28) MUTATED                                           1   182
  AMP PEAK 33(XQ28) WILD-TYPE                                         0   293
D33V7, multiclass
                                           clus
vv                                          AMP PEAK 33(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             6
  BLACK OR AFRICAN AMERICAN                                        11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           182
                                           clus
vv                                          AMP PEAK 33(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              12
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             293
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                             cls
clus                            0   1
  AMP PEAK 33(XQ28) MUTATED     6 131
  AMP PEAK 33(XQ28) WILD-TYPE   4 194
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 33(XQ28) MUTATED      6  131
  AMP PEAK 33(XQ28) WILD-TYPE    4  194
                        clus
vv                       AMP PEAK 33(XQ28) MUTATED AMP PEAK 33(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             6                           4
  NOT HISPANIC OR LATINO                       131                         194
[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   129 130
  DEL PEAK  1(1P36.11) WILD-TYPE 137 160
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           259                            297 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           130                            160 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 TCGA-04-1350 
       40.24         1.81         2.01        46.62        65.52        63.98 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 TCGA-04-1514 
       65.46        49.28        32.52        33.67        71.47        56.55 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       19.99       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0369 TCGA-09-1659 
       64.64        36.23        47.70        29.16        35.57         9.99 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        41.62        57.60        55.36        30.51 
TCGA-09-1670 TCGA-09-1672 TCGA-09-2048 TCGA-09-2049 TCGA-09-2055 TCGA-09-2056 
       17.98         5.85         4.54       112.41        26.93        12.46 
TCGA-10-0925 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 TCGA-10-0937 
       54.31        18.51        33.24        32.28        35.44        15.12 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
        2.73        12.39         2.50        11.38        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0794 TCGA-13-0801 TCGA-13-0802 
       32.25        31.04        21.40        30.35         8.28         8.19 
TCGA-13-0803 TCGA-13-0883 TCGA-13-0886 TCGA-13-0887 TCGA-13-0890 TCGA-13-0900 
       43.86        68.94        74.27        66.67        67.99        57.07 
TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0912 TCGA-13-0913 
       47.38        47.84        44.94        44.84        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0924 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
       21.17        14.89         6.08         5.92         6.84         4.70 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1485 
        5.33        54.64        87.06        61.71        98.04        20.68 
TCGA-13-1487 TCGA-13-1491 TCGA-13-1494 TCGA-13-1497 TCGA-13-1505 TCGA-13-1506 
       22.39        52.44        38.20        54.31         4.21         4.41 
TCGA-13-1509 TCGA-13-1510 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        4.18         2.56        12.23        10.78         8.75        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 TCGA-20-1685 TCGA-20-1686 
        8.42        23.05        26.20        27.52        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1027 TCGA-23-1029 
        2.66        47.54        42.54        40.54        31.76         8.81 
TCGA-23-1031 TCGA-23-1110 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-2078 
       18.90        54.51        86.01       129.96         4.27        87.48 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
       49.84         2.76         4.70        21.80         7.66        54.12 
TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
       47.41         6.31         7.82         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
        5.95         4.83        43.53        72.92        12.46         9.11 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1557 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       57.40        64.27        39.88        25.87        10.26        17.23 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       48.33        38.24         8.32         3.81         4.37        11.28 
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-24-2020 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2254 TCGA-24-2271 
      152.02        58.16       109.71        14.43        57.07        31.63 
TCGA-24-2288 TCGA-24-2290 TCGA-25-1313 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 
        0.82        36.23        26.96        37.02         1.02        36.95 
TCGA-25-1323 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       12.00         0.36         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2396 
       35.54        24.99        18.05        85.05        49.05         3.02 
TCGA-25-2398 TCGA-25-2400 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 
       45.01        42.02        31.00        78.90        44.71       101.79 
TCGA-29-1696 TCGA-29-1705 TCGA-29-1707 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       33.70        18.25        41.98        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       12.36        11.84         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2436 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       62.47         4.90         9.76        51.91        36.26         2.47 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1891 TCGA-31-1955 TCGA-31-1956 
       48.10        44.91        34.78        30.05        42.51        44.12 
TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
        2.20        28.77        29.10        30.08        25.74        24.23 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 
       33.01        29.82        25.91        25.08        23.80        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-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 TCGA-57-1992 TCGA-59-2350 
        9.44        42.02         7.46        21.14        29.00        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-61-1734 TCGA-61-1737 TCGA-61-1740 
        8.09        31.43        18.54        28.47        44.84         2.43 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 
       11.41        13.02        48.92        67.76        43.43        15.75 
TCGA-61-1919 TCGA-61-1998 TCGA-61-2003 TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 
       38.17         5.52         4.01        39.85        45.96        45.40 
TCGA-61-2087 TCGA-61-2092 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2612 
        4.80        51.72        60.62        65.52        55.50         6.35 
TCGA-61-2614 
        8.61 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 
       41.00        49.15        18.51        11.87        63.09        48.76 
TCGA-04-1349 TCGA-04-1362 TCGA-04-1365 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 
       21.57        44.32        76.57        82.39        41.59        38.37 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1652 TCGA-04-1655 TCGA-09-0365 TCGA-09-0366 
       27.88        28.64        31.86        45.37         9.47        57.76 
TCGA-09-0367 TCGA-09-1661 TCGA-09-1667 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       17.98        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-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 
       20.94        25.91        81.47        11.70         3.91        35.80 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0726 
       19.86         6.21        24.59        44.55        39.58        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0768 TCGA-13-0791 
       15.19        17.82        55.17        11.18         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 
       36.72        28.70        19.59         8.71         7.79         8.12 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0888 
       35.28        35.28        13.61       107.18        91.40        70.39 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 
       61.84        69.01        43.36        57.47        56.15        19.36 
TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       48.33        37.08        27.72        13.81         4.64         6.41 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1411 TCGA-13-1483 
       10.88         6.61         7.36         6.05         4.21        29.42 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       70.82        82.88        73.55        49.25         4.24        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1507 TCGA-13-1511 
       38.40        13.97        32.84        16.57         4.77         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 TCGA-20-0990 TCGA-20-0996 
        3.09        14.24         8.61         6.28        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 
        2.24        51.35         3.22        31.20        68.68         4.57 
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-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 TCGA-24-1416 
       19.66        11.64        41.56        22.32        63.55         6.38 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        7.99         7.86         5.36        17.39        28.37        19.17 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       18.67         8.55        45.14       105.99         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 
       22.22        26.96        16.21        56.58        41.06        51.91 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 
       41.39        58.09        88.50        70.62        19.53        44.09 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 TCGA-24-1844 
       45.50        47.70        90.15        88.37         3.48         3.72 
TCGA-24-1849 TCGA-24-1923 TCGA-24-2019 TCGA-24-2023 TCGA-24-2026 TCGA-24-2030 
        5.79        22.68         4.87        44.84        34.82        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 
       18.48        28.18        64.01        44.52        36.16         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 TCGA-24-2293 
        0.36        47.54        70.45        44.61        67.36        16.64 
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        32.02        51.06 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       34.98        65.00        33.96         2.99         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1635 TCGA-25-1870 TCGA-25-2042 
       18.02        15.81        20.61        51.22        14.96        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
        1.02        38.04        12.00        19.99         2.96        29.03 
TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       26.99        47.18        38.53         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1711 
        0.53        16.90        18.67        59.67        29.23        34.62 
TCGA-29-1766 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-2428 
       39.12        12.30        14.93         8.38         7.23        45.11 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1856 
       42.25        11.84        11.47        21.04        38.07        15.68 
TCGA-30-1857 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
        0.26         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-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1578 TCGA-36-1581 
       21.53        22.85        22.55         8.55        27.85        24.69 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2548 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 
       35.05        29.49        14.17        16.18         7.99        26.04 
TCGA-42-2587 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 
       23.74        40.77         1.48        24.03        11.38         1.74 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-A5PD 
       22.32        25.08        25.02       180.20        80.12        20.52 
TCGA-61-1721 TCGA-61-1724 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       11.11        20.94        27.88         4.34        31.79        48.79 
TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       35.80        33.67        43.69         1.45         8.42         5.79 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 
        9.07        34.13        31.30        37.05        42.51        56.61 
TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2008 TCGA-61-2012 TCGA-61-2016 
        2.01        14.50        17.98        30.64        30.64         1.18 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2102 TCGA-61-2104 
        4.77        71.74        61.64        58.39         6.48        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-OY-A56P 
       20.68        44.52       125.75        22.22        31.07        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

  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 
                        152.02                         180.20 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         29.82                          26.83 
[1] "0.3 - 152.0 (29.8)" "0.3 - 180.2 (26.8)"
[1] "hr=" "1.2"
D34V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  1(1P36.11) MUTATED         1   263                0
  DEL PEAK  1(1P36.11) WILD-TYPE       1   294                2
D34V3, multiclass
                  clus
vv                 DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     263                            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, continuous
D34V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     1 264
  DEL PEAK  1(1P36.11) WILD-TYPE   2 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      1  264
  DEL PEAK  1(1P36.11) WILD-TYPE    2  304
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             1                              2
  YES                          264                            304
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.11) MUTATED    8 16  2  1
  DEL PEAK  1(1P36.11) WILD-TYPE  6 10  3  2
D34V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                            8                              6
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.11) MUTATED                                  0     8
  DEL PEAK  1(1P36.11) WILD-TYPE                                3    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.11) MUTATED                          12
  DEL PEAK  1(1P36.11) WILD-TYPE                        20
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.11) MUTATED                                           0
  DEL PEAK  1(1P36.11) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.11) MUTATED     224
  DEL PEAK  1(1P36.11) WILD-TYPE   251
D34V7, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                           12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              224
                                           clus
vv                                          DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 10
  BLACK OR AFRICAN AMERICAN                                             20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                251
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     6 150
  DEL PEAK  1(1P36.11) WILD-TYPE   4 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      6  150
  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                          150
                        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    42  48
  DEL PEAK  2(1Q41) WILD-TYPE 224 242
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         90                         466 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                         48                         242 
$`DEL PEAK  2(1Q41) MUTATED`
TCGA-04-1338 TCGA-04-1349 TCGA-04-1362 TCGA-04-1517 TCGA-04-1536 TCGA-04-1651 
       46.62        21.57        44.32        19.99        29.10        36.23 
TCGA-04-1654 TCGA-09-0367 TCGA-09-1675 TCGA-09-2050 TCGA-09-2051 TCGA-10-0928 
       47.70        17.98        97.55        71.11        63.09        18.51 
TCGA-10-0930 TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 TCGA-13-0755 TCGA-13-0792 
       33.24         6.21        44.55        31.10         2.50        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0807 TCGA-13-0885 TCGA-13-0893 TCGA-13-0900 
       28.70        30.35        13.61        91.40        43.36        57.07 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1497 
        6.05         5.92        20.68        70.82        73.55        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-2059 TCGA-13-2065 TCGA-20-0987 TCGA-20-1687 
       37.61        38.40        12.23         8.75        23.05         2.66 
TCGA-23-1022 TCGA-23-1029 TCGA-23-1032 TCGA-23-1109 TCGA-23-1117 TCGA-23-1121 
       42.54         8.81         2.24        51.35        33.30         6.38 
TCGA-23-1124 TCGA-23-2641 TCGA-23-2645 TCGA-24-0968 TCGA-24-0979 TCGA-24-1103 
       58.13         2.76         4.50        19.66        41.56        54.12 
TCGA-24-1418 TCGA-24-1425 TCGA-24-1428 TCGA-24-1435 TCGA-24-1466 TCGA-24-1567 
        7.99         5.95        17.39        43.53        45.14        17.23 
TCGA-24-1844 TCGA-24-1920 TCGA-24-2020 TCGA-24-2026 TCGA-24-2280 TCGA-25-1314 
        3.72         9.80       152.02        34.82        70.45        32.02 
TCGA-25-1315 TCGA-25-1632 TCGA-25-2391 TCGA-25-2409 TCGA-29-1691 TCGA-29-1705 
       51.06        56.94        49.05        26.99        47.18        18.25 
TCGA-29-1707 TCGA-29-1763 TCGA-29-1768 TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 
       41.98        66.81        31.23        11.84         8.38         7.23 
TCGA-30-1718 TCGA-30-1891 TCGA-36-2548 TCGA-42-2591 TCGA-57-1582 TCGA-57-1585 
       51.91        30.05        14.17        40.77        24.03         1.74 
TCGA-59-2348 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1737 TCGA-61-1895 TCGA-61-1901 
      180.20        20.52        20.94        44.84         1.45        11.41 
TCGA-61-1907 TCGA-61-1914 TCGA-61-2012 TCGA-61-2102 TCGA-61-2612 TCGA-WR-A838 
       31.30        56.61        30.64         6.48         6.35         8.05 

$`DEL PEAK  2(1Q41) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       40.24        41.00         1.81        49.15         2.01        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 
       11.87        65.52        63.09        48.76        63.98        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        33.67        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       56.55        41.59        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 
       48.89        27.88        28.64        64.64        31.86        45.37 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        57.76        35.57         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 
       26.93        12.46        54.31        25.91        81.47        32.28 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       11.70         3.91        35.44        35.80        15.12        19.86 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 
       24.59        39.58         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        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0795 TCGA-13-0797 
       31.04        21.40         8.45        38.93        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.28        68.94       107.18        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 
       61.84        67.99        69.01        57.47        56.15        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 
       47.38        48.33        47.84        44.94        44.84        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.84         4.70         4.21         5.33        54.64        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 
       61.71        29.42        98.04        22.39        82.88        52.44 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       38.20        49.25         4.24        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT 
        3.09        14.24         8.61        10.78         6.28        54.77 
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-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 
       19.10        16.70         2.93        47.54        40.54        15.39 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1031 TCGA-23-1110 
       26.83        31.76        49.41        29.13        18.90        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         4.57        86.01       129.96 
TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
        4.27        39.09        33.47         0.53        24.95       115.89 
TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-24-0966 
       87.48        91.66        77.00        49.84         4.70         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 
       11.64        21.80         7.66        22.32        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-24-1426 TCGA-24-1427 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        6.02         5.36         4.83        28.37        19.17        18.67 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
        8.55        72.92        12.46       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-24-1553 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-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 
       25.87        10.26        90.15        88.37        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 
        8.32         3.48         3.81         4.37        11.28         5.79 
TCGA-24-1850 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        5.52        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 
        4.87        44.84        58.16       109.71        14.43        53.95 
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-24-2281 TCGA-24-2288 
        0.79         0.36        47.54        31.63        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-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 
        1.02        26.96        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
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-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       78.90        44.71       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32         0.53        16.90        18.67        59.67 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       29.23        34.62        17.00        85.68        62.93        39.12 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       22.98        24.36        22.55        17.33        12.36        12.30 
TCGA-29-1778 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       14.93         5.36        34.62        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         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       21.04        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-30-1892 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 
       57.57        24.26        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-36-1569 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-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       25.74        27.85        24.23        24.69        35.05        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-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
        2.24        20.98        18.31        20.52         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       11.47         7.99        26.04        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 
        7.46         1.48        11.38        21.14        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-59-2355 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-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       31.43        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 
       48.79        35.80         2.43        33.67        43.69         8.42 
TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 
        5.79        13.02         9.07        34.13        37.05        42.51 
TCGA-61-1913 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       48.92        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 
        5.52        14.50        17.98         4.01        30.64        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-61-2101 
       71.74        61.64        58.39        60.62        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-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
        8.61        39.68        18.94         0.79 

  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                       1.45                        0.26 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                     180.20                      129.96 
  DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE 
                     30.495                      27.620 
[1] "1.4 - 180.2 (30.5)" "0.3 - 130.0 (27.6)"
[1] "hr=" "1"  
D35V2, continuous
                             vv
clus                          OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  2(1Q41) MUTATED         0    91                0
  DEL PEAK  2(1Q41) WILD-TYPE       2   466                2
D35V3, multiclass
                  clus
vv                 DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  OMENTUM                                  0                           2
  OVARY                                   91                         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, continuous
D35V5, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q41) MUTATED     1  93
  DEL PEAK  2(1Q41) WILD-TYPE   2 475
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED      1   93
  DEL PEAK  2(1Q41) WILD-TYPE    2  475
     clus
vv    DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  NO                          1                           2
  YES                        93                         475
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  2(1Q41) MUTATED    0  3  0  0
  DEL PEAK  2(1Q41) WILD-TYPE 14 23  5  3
D35V6, multiclass
    clus
vv   DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  R0                         0                          14
  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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1Q41) MUTATED                                  0     1
  DEL PEAK  2(1Q41) WILD-TYPE                                3    17
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1Q41) MUTATED                           9
  DEL PEAK  2(1Q41) WILD-TYPE                        23
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  2(1Q41) MUTATED                                           1    75
  DEL PEAK  2(1Q41) WILD-TYPE                                         0   400
D35V7, multiclass
                                           clus
vv                                          DEL PEAK  2(1Q41) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             1
  BLACK OR AFRICAN AMERICAN                                         9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                            75
                                           clus
vv                                          DEL PEAK  2(1Q41) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                          23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             400
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q41) MUTATED     0  54
  DEL PEAK  2(1Q41) WILD-TYPE  10 271
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q41) MUTATED      0   54
  DEL PEAK  2(1Q41) WILD-TYPE   10  271
                        clus
vv                       DEL PEAK  2(1Q41) MUTATED DEL PEAK  2(1Q41) WILD-TYPE
  HISPANIC OR LATINO                             0                          10
  NOT HISPANIC OR LATINO                        54                         271
[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    53  64
  DEL PEAK  3(2P25.3) WILD-TYPE 213 226
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                          117                           439 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           64                           226 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-04-1331 TCGA-04-1343 TCGA-04-1348 TCGA-04-1356 TCGA-04-1362 TCGA-04-1514 
       40.24        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-10-0928 TCGA-10-0930 TCGA-10-0938 TCGA-13-0714 TCGA-13-0751 TCGA-13-0758 
       18.51        33.24        19.86         6.21        55.17        11.38 
TCGA-13-0762 TCGA-13-0794 TCGA-13-0803 TCGA-13-0883 TCGA-13-0886 TCGA-13-0889 
       32.25        30.35        43.86        68.94        74.27        61.84 
TCGA-13-0891 TCGA-13-0904 TCGA-13-0916 TCGA-13-0923 TCGA-13-1408 TCGA-13-1411 
       69.01        48.33        21.17         6.41         5.92         4.21 
TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       98.04        70.82        82.88        37.61        38.40        32.84 
TCGA-13-1509 TCGA-13-1510 TCGA-20-0990 TCGA-23-1022 TCGA-23-1029 TCGA-23-1119 
        4.18         2.56        25.94        42.54         8.81       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-2077 TCGA-23-2078 
        4.27         6.38        33.47        58.13       115.89        87.48 
TCGA-24-1103 TCGA-24-1413 TCGA-24-1430 TCGA-24-1436 TCGA-24-1464 TCGA-24-1546 
       54.12         6.31        28.37         8.55        12.46        64.27 
TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 
       70.62        39.88        19.53        48.33         8.32         3.72 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1930 TCGA-24-2033 TCGA-24-2254 
       11.28         5.79        22.68        81.11        18.48        57.07 
TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 TCGA-25-1321 
       47.54        70.45         0.82        36.23        53.26        33.96 
TCGA-25-1329 TCGA-25-1630 TCGA-25-1878 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 
        2.96         7.86        85.05         1.02         3.02        12.00 
TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1695 TCGA-29-1699 
        2.96        26.99        78.90       101.79         0.79         0.53 
TCGA-29-1769 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-30-1718 TCGA-30-1855 
       22.98        42.25        11.84        11.47        51.91         2.47 
TCGA-30-1861 TCGA-36-1574 TCGA-36-1577 TCGA-36-1581 TCGA-36-2545 TCGA-36-2547 
       34.78        22.55        25.74        24.69        18.31        20.52 
TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2591 TCGA-57-1582 TCGA-57-1993 
        6.05        16.18        26.04        40.77        24.03        25.08 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1740 TCGA-61-1741 
       20.94        18.54        27.88        28.47         2.43        33.67 
TCGA-61-1743 TCGA-61-1917 TCGA-61-1918 TCGA-61-2002 TCGA-61-2016 TCGA-61-2018 
       43.69        43.43        15.75        17.98         1.18        45.40 
TCGA-61-2087 TCGA-61-2096 TCGA-61-2109 
        4.80        58.39        20.68 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       41.00         1.81        49.15         2.01        46.62        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 
       65.52        63.09        21.57        63.98        65.46        32.52 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 
       33.67        76.57        71.47        82.39        41.59        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-09-0364 TCGA-09-0365 
       36.23        31.86        47.70        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 
       17.98         5.85         8.55        97.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 
       12.46        54.31        25.91        81.47        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 TCGA-13-0720 
        3.91        35.44        35.80        15.12        24.59        44.55 
TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       39.58         2.73        12.39        31.10        15.19        17.82 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.54        34.06        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 
        8.45        38.93        36.72        28.70        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
        7.79         8.12         8.28         8.19        35.28        35.28 
TCGA-13-0807 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
       13.61       107.18        91.40        66.67        70.39        67.99 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       43.36        57.47        56.15        57.07        19.36        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 
       29.98        14.89        13.81         4.64         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        6.61         7.36         6.05         6.84         4.70         5.33 
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-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 
       13.97        16.57         4.21         4.41         4.77         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.09        14.24        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 
        6.28        54.77         8.42        23.05        26.20        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-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.24        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1122 
       31.20        68.68         4.57        33.30        86.01        39.09 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 
        0.53        24.95        91.66        77.00        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 
       41.56         7.66        22.32        63.55        47.41         6.38 
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-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 
        5.95         5.36         4.83        17.39        19.17        18.67 
TCGA-24-1435 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 
       43.53        72.92        45.14       105.99         9.11         3.45 
TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        1.18        22.22        26.96        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1560 
       41.06        51.91        41.39        58.09        88.50        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-24-1843 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 
       88.37        38.24         3.48         3.81         4.37         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 
        9.80        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        53.95 
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-24-2271 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-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 
       34.98        65.00        36.95         2.99        12.00        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       18.02        15.81         0.36        20.61         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       13.02        49.05        38.04        45.01        19.99        42.02 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 
       29.03        31.00        44.71        47.18        38.53        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32        16.90        18.67        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        29.23        34.62        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       62.93        39.12        31.23        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        34.62        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 
        4.90         9.76        21.04        38.07        36.26        15.68 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
        0.26        48.10        44.91         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-31-1953 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-36-1575 TCGA-36-1576 
       28.77        29.10        21.53        22.85         8.55        30.08 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       27.85        24.23        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-36-2548 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       14.17        11.47         7.99        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        7.46         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-59-A5PD 
        9.40        34.39         2.14         5.42        44.81        20.52 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 
       11.11         8.09        31.43         4.34        31.79        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       44.84        35.80         1.45         8.42         5.79        11.41 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        38.17         2.01         5.52 
TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2017 
       14.50         4.01        30.64        39.85        30.64        45.96 
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-61-2102 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-61-2613 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 
        8.05 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.53                          0.26 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       129.96                        180.20 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                        26.04                         28.70 
[1] "0.5 - 130.0 (26.0)" "0.3 - 180.2 (28.7)"
[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       1   439                2
D36V3, multiclass
                  clus
vv                 DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  OMENTUM                                    1                             1
  OVARY                                    118                           439
  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, continuous
D36V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     1 119
  DEL PEAK  3(2P25.3) WILD-TYPE   2 449
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      1  119
  DEL PEAK  3(2P25.3) WILD-TYPE    2  449
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                            1                             2
  YES                         119                           449
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(2P25.3) MUTATED    7  3  0  0
  DEL PEAK  3(2P25.3) WILD-TYPE  7 23  5  3
D36V6, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                           7                             7
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2P25.3) MUTATED                                  0     3
  DEL PEAK  3(2P25.3) WILD-TYPE                                3    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(2P25.3) MUTATED                           2
  DEL PEAK  3(2P25.3) WILD-TYPE                        30
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2P25.3) MUTATED                                           0   108
  DEL PEAK  3(2P25.3) WILD-TYPE                                         1   367
D36V7, multiclass
                                           clus
vv                                          DEL PEAK  3(2P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                           2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             108
                                           clus
vv                                          DEL PEAK  3(2P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               367
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     3  69
  DEL PEAK  3(2P25.3) WILD-TYPE   7 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      3   69
  DEL PEAK  3(2P25.3) WILD-TYPE    7  256
                        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                           256
[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    66  65
  DEL PEAK  4(2Q22.1) WILD-TYPE 200 225
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          131                           425 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           65                           225 
$`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-09-0367 TCGA-09-1665 
       33.67        19.99        36.23        47.70        17.98        41.62 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2048 TCGA-09-2054 TCGA-10-0928 TCGA-13-0724 
        3.02         8.55         4.54        20.94        18.51         2.73 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0758 TCGA-13-0764 TCGA-13-0791 TCGA-13-0792 
       12.39        31.10        11.38        31.04        38.93        36.72 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0807 TCGA-13-0885 TCGA-13-0886 TCGA-13-0890 
        7.79         8.12        13.61        91.40        74.27        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0911 TCGA-13-0913 TCGA-13-0921 
       69.01        43.36        57.07        27.72        29.98         4.64 
TCGA-13-0924 TCGA-13-1404 TCGA-13-1411 TCGA-13-1484 TCGA-13-1491 TCGA-13-1494 
        6.08         6.61         4.21        98.04        52.44        38.20 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1506 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 
       54.31        37.61         4.41         6.28         8.42        23.05 
TCGA-20-0991 TCGA-20-1682 TCGA-20-1686 TCGA-23-1031 TCGA-23-1116 TCGA-23-1117 
       26.20        27.52         2.93        18.90         4.57        33.30 
TCGA-23-1121 TCGA-23-2641 TCGA-23-2645 TCGA-24-1104 TCGA-24-1413 TCGA-24-1417 
        6.38         2.76         4.50        63.55         6.31         7.82 
TCGA-24-1428 TCGA-24-1469 TCGA-24-1474 TCGA-24-1546 TCGA-24-1555 TCGA-24-1557 
       17.39         9.11        22.22        64.27        88.50        39.88 
TCGA-24-1558 TCGA-24-1563 TCGA-24-1614 TCGA-24-1846 TCGA-24-1847 TCGA-24-1920 
       19.53        47.70        48.33         4.37        11.28         9.80 
TCGA-24-1923 TCGA-24-2029 TCGA-24-2260 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
       22.68        14.43        36.16        44.61         0.82        67.36 
TCGA-25-1318 TCGA-25-1323 TCGA-25-1627 TCGA-25-1635 TCGA-25-2392 TCGA-25-2398 
       34.98        12.00         0.36        51.22         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         0.79         0.53        16.90 
TCGA-29-1702 TCGA-29-1710 TCGA-29-1761 TCGA-29-1763 TCGA-29-1770 TCGA-29-1774 
       18.67        29.23        17.00        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 
        4.80        51.72         6.48        20.68         8.61 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24        41.00         1.81         2.01        18.51        11.87 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1365 
       63.09        48.76        63.98        65.46        32.52        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       71.47        82.39        56.55        41.59        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-09-0364 TCGA-09-0365 TCGA-09-0366 
       64.64        31.86        45.37        29.16         9.47        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 
       35.57         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-09-1675 
       61.87        55.36        30.51        17.98         5.85        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-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       39.75        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       15.12        19.86         6.21        24.59        44.55        39.58 
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-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0793 TCGA-13-0794 
       34.06        32.25        21.40         8.45        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
       19.59         8.71         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       35.28        68.94       107.18        66.67        70.39        61.84 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
       44.94        44.84        37.08        34.06        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
       13.81         6.41        10.88         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 
        6.84         4.70         5.33        54.64        87.06        61.71 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 
       29.42        20.68        22.39        70.82        82.88        73.55 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       49.25         4.24        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.21         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       14.24        12.23         8.61        10.78         8.75        54.77 
TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       25.94        72.20        25.38        19.10        16.70         2.66 
TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
       47.54        42.54        40.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       49.41         8.81        29.13         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
        3.22        31.20        68.68        86.01       129.96         4.27 
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-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-24-0966 
       87.48        91.66        77.00        49.84         4.70         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
       19.66        11.64        21.80        41.56         7.66        22.32 
TCGA-24-1103 TCGA-24-1105 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       54.12        47.41         6.38         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 
       19.17        18.67        43.53         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 
       45.14       105.99         3.45         1.18        26.96        57.40 
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-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       70.62        44.09        45.50        25.87        10.26        17.23 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       90.15        88.37        38.24         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        3.81         5.79         5.52        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       81.11         4.87       152.02        44.84        58.16        34.82 
TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
      109.71        53.95        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 
       57.07         0.79         0.36        47.54        31.63        70.45 
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-25-1317 TCGA-25-1319 
       26.96        32.02        51.06        37.02         1.02        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       36.95        33.96         2.99         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
       15.81        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       35.54        14.96        24.99        18.05        85.05        13.02 
TCGA-25-2391 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 
       49.05        38.04         3.02        12.00        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 
        2.96        29.03        31.00        44.71        47.18        38.53 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       33.70        31.20        68.32        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 
       34.62        85.68        62.93        39.12        31.23        22.98 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.55        12.36        11.84        12.30        14.93         8.38 
TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        7.23         5.36        34.62        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
        4.90        42.25        11.84         9.76        21.04        38.07 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 
       51.91         2.47        15.68         0.26        48.10         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       36.62         1.22        57.57        30.05        48.79        45.57 
TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 
       30.18        18.77         6.71        42.51        44.12         2.20 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
       28.77        29.10        21.53        22.85        22.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 
       25.74        27.85        24.23        33.01        25.91        23.80 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 
       21.60        20.98        20.52        14.17         6.05        11.47 
TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        7.99        26.04         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
        1.48        24.03        11.38        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 
       25.02       180.20        80.12       116.12        34.39         2.14 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 
       44.81        20.52        11.11         8.09        20.94        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 
       27.88         4.34        31.79        28.47        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-61-1910 TCGA-61-1914 
       11.41        13.02         9.07        34.13        37.05        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 
       17.98         4.01        30.64        30.64        45.96        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-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 
       55.50        76.87        44.52       125.75        22.22         6.35 
TCGA-61-2613 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       31.07        39.68        18.94         0.79         8.05 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.36                          0.26 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       101.79                        180.20 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        23.74                         29.10 
[1] "0.4 - 101.8 (23.7)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1.1"
D37V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  4(2Q22.1) MUTATED         0   131                1
  DEL PEAK  4(2Q22.1) WILD-TYPE       2   426                1
D37V3, multiclass
                  clus
vv                 DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    131                           426
  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, continuous
D37V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     0 134
  DEL PEAK  4(2Q22.1) WILD-TYPE   3 434
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      0  134
  DEL PEAK  4(2Q22.1) WILD-TYPE    3  434
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            0                             3
  YES                         134                           434
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  4(2Q22.1) MUTATED    4 10  1  0
  DEL PEAK  4(2Q22.1) WILD-TYPE 10 16  4  3
D37V6, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                           4                            10
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q22.1) MUTATED                                  0     5
  DEL PEAK  4(2Q22.1) WILD-TYPE                                3    13
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q22.1) MUTATED                           6
  DEL PEAK  4(2Q22.1) WILD-TYPE                        26
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q22.1) MUTATED                                           1   110
  DEL PEAK  4(2Q22.1) WILD-TYPE                                         0   365
D37V7, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                           6
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             110
                                           clus
vv                                          DEL PEAK  4(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                13
  BLACK OR AFRICAN AMERICAN                                            26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               365
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     5  75
  DEL PEAK  4(2Q22.1) WILD-TYPE   5 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      5   75
  DEL PEAK  4(2Q22.1) WILD-TYPE    5  250
                        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                           250
[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    93  75
  DEL PEAK  5(2Q37.3) WILD-TYPE 173 215
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          168                           388 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           75                           215 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-04-1336 TCGA-04-1338 TCGA-04-1349 TCGA-04-1516 TCGA-04-1536 TCGA-04-1646 
       49.15        46.62        21.57        41.59        29.10        27.88 
TCGA-09-0369 TCGA-09-1668 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 
       35.57        55.36        30.51         3.02         8.55         6.12 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0934 TCGA-13-0717 TCGA-13-0720 
       18.51        33.24        32.28         3.91        24.59        44.55 
TCGA-13-0723 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 
       39.58        55.17        11.38        11.54        34.06        32.25 
TCGA-13-0799 TCGA-13-0801 TCGA-13-0803 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
        7.79         8.28        43.86        67.99        69.01        43.36 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 
       48.33        47.84        44.84        21.17        13.81         6.41 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1484 
        6.61         7.36         4.21         5.33        87.06        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1494 TCGA-13-1497 TCGA-13-1501 TCGA-13-1505 
       22.39        70.82        38.20        54.31        32.84         4.21 
TCGA-13-1506 TCGA-13-1512 TCGA-13-2060 TCGA-13-2061 TCGA-20-0991 TCGA-20-1682 
        4.41         3.09         8.61        10.78        26.20        27.52 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1026 TCGA-23-1028 TCGA-23-1031 TCGA-23-1032 
        2.93         2.66        26.83        49.41        18.90         2.24 
TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1121 
       54.51        68.68         4.57        33.30        86.01         6.38 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-23-2084 TCGA-23-2641 TCGA-24-0968 
       39.09        58.13       115.89        49.84         2.76        19.66 
TCGA-24-0982 TCGA-24-1103 TCGA-24-1413 TCGA-24-1417 TCGA-24-1425 TCGA-24-1427 
       22.32        54.12         6.31         7.82         5.95         4.83 
TCGA-24-1428 TCGA-24-1434 TCGA-24-1436 TCGA-24-1470 TCGA-24-1552 TCGA-24-1553 
       17.39        18.67         8.55         3.45        41.39        58.09 
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-24-2027 TCGA-24-2260 TCGA-24-2280 
       22.68         4.87       152.02       109.71        36.16        70.45 
TCGA-24-2290 TCGA-25-1314 TCGA-25-1318 TCGA-25-1625 TCGA-25-1627 TCGA-25-1630 
       36.23        32.02        34.98        18.02         0.36         7.86 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       51.22        18.05         2.96        26.99        78.90        47.18 
TCGA-29-1693 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
      101.79         0.53        16.90        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1781 TCGA-29-1784 
       34.62        22.98        24.36        17.33         8.38         5.36 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1860 TCGA-30-1861 TCGA-30-1887 
       51.91        36.26         2.47        44.91        34.78        24.26 
TCGA-30-1891 TCGA-31-1951 TCGA-31-1953 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       30.05        22.49         6.71        22.55         8.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2537 TCGA-36-2543 
       27.85        24.23        24.69        35.05        25.91         2.24 
TCGA-36-2545 TCGA-36-2547 TCGA-3P-A9WA TCGA-42-2588 TCGA-42-2589 TCGA-42-2591 
       18.31        20.52         7.99         9.44        42.02        40.77 
TCGA-57-1585 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-A5PD TCGA-61-1724 
        1.74        25.08        25.02       116.12        20.52        20.94 
TCGA-61-1728 TCGA-61-1738 TCGA-61-1740 TCGA-61-1900 TCGA-61-1903 TCGA-61-1907 
       27.88        35.80         2.43         5.79        13.02        31.30 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-2012 TCGA-61-2016 TCGA-61-2087 
       48.92        56.61        43.43        30.64         1.18         4.80 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2104 TCGA-61-2109 TCGA-61-2612 TCGA-61-2614 
       51.72        71.74        76.87        20.68         6.35         8.61 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24        41.00         1.81         2.01        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        48.76        63.98        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        71.47        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1638 
       56.55        19.99        38.37       119.08        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       48.89        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 
       45.37        29.16         9.47        57.76        17.98         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0933 TCGA-10-0935 
       12.46        54.31        25.91        81.47        11.70        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0724 TCGA-13-0725 
       35.80        15.12        19.86         6.21         2.73        12.39 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0764 
       31.10        15.19        17.82         2.50        11.18        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
       19.59         8.71         8.12         8.19        35.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0889 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       70.39        61.84        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       47.38        44.94        37.08        27.72        34.06        29.98 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 TCGA-13-1408 
       14.89         4.64         6.08        10.88         6.05         5.92 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        6.84         4.70        54.64        61.71        29.42        20.68 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       82.88        52.44        73.55        49.25         4.24        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       38.40        13.97        16.57         4.77         4.18         2.56 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
        3.91        14.24        12.23         8.75         6.28        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 TCGA-20-1684 
        8.42        23.05        25.94        72.20        25.38        19.10 
TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 
       16.70        47.54        42.54        40.54        15.39        31.76 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 
        8.81        29.13        51.35         3.22        31.20       129.96 
TCGA-23-1120 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
        4.27        33.47         0.53        24.95        87.48        91.66 
TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0975 
       77.00         4.70         4.50         7.63        11.64        21.80 
TCGA-24-0979 TCGA-24-0980 TCGA-24-1104 TCGA-24-1105 TCGA-24-1416 TCGA-24-1418 
       41.56         7.66        63.55        47.41         6.38         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 
        7.86         0.76         6.25         6.02         5.36        28.37 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 
       19.17        43.53        72.92        12.46        45.14       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1557 
       16.21        56.58        41.06        51.91        88.50        39.88 
TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 
       19.53        44.09        45.50        25.87        10.26        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-24-1844 TCGA-24-1846 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 
        3.72         4.37         9.80        30.21        16.44        11.05 
TCGA-24-1930 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 
       81.11        44.84        58.16        34.82        14.43        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 
       18.48        28.18        64.01        44.52        57.07         0.79 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.36        47.54        31.63        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-25-1319 TCGA-25-1320 TCGA-25-1321 
       51.06        37.02         1.02        65.00        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 
        2.99        12.00         2.96        18.58        15.81        20.61 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 
        0.30        56.94        60.59        35.54        14.96        24.99 
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-25-2404 TCGA-25-2408 
       12.00        45.01        19.99        42.02        29.03        31.00 
TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
       44.71        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1702 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       18.67        29.23        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       39.12        31.23        22.55        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       14.93         7.23        34.62        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         4.90        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 
       21.04        38.07        15.68         0.26        48.10         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       36.62         1.22        57.57        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 
       18.77        42.51        44.12         2.20        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-2530 TCGA-36-2532 TCGA-36-2534 
       21.53        22.85        30.08        33.01        29.49        29.82 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 
       25.08        23.80        21.60        20.98        14.17         6.05 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2590 TCGA-42-2593 
       16.18        11.47        26.04        23.74         7.46         1.48 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 
       24.03        11.38        21.14        22.32        29.00       180.20 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1730 
       44.81        11.11         8.09        31.43        18.54         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 
       31.79        28.47        48.79        44.84        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 
        1.45         8.42        11.41         9.07        34.13        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       42.51        67.76        15.75        38.17         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-61-2018 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       45.40         4.77        61.64        58.39        60.62        65.52 
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-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.36                          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 
                       24.855                        29.195 
[1] "0.4 - 152.0 (24.9)" "0.3 - 180.2 (29.2)"
[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       1   389                1
D38V3, multiclass
                  clus
vv                 DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  OMENTUM                                    1                             1
  OVARY                                    168                           389
  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, continuous
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     2 170
  DEL PEAK  5(2Q37.3) WILD-TYPE   1 398
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      2  170
  DEL PEAK  5(2Q37.3) WILD-TYPE    1  398
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                            2                             1
  YES                         170                           398
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  5(2Q37.3) MUTATED    5  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                           5                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q37.3) MUTATED                                  0     6
  DEL PEAK  5(2Q37.3) WILD-TYPE                                3    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q37.3) MUTATED                          12
  DEL PEAK  5(2Q37.3) WILD-TYPE                        20
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q37.3) MUTATED                                           0   140
  DEL PEAK  5(2Q37.3) WILD-TYPE                                         1   335
D38V7, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             140
                                           clus
vv                                          DEL PEAK  5(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               335
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     3  97
  DEL PEAK  5(2Q37.3) WILD-TYPE   7 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      3   97
  DEL PEAK  5(2Q37.3) WILD-TYPE    7  228
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           228
[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    98 102
  DEL PEAK  6(3P26.2) WILD-TYPE 168 188
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          200                           356 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                          102                           188 
$`DEL PEAK  6(3P26.2) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1356 
       40.24        49.15        65.52        63.09        65.46        49.28 
TCGA-04-1365 TCGA-04-1371 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       76.57        82.39        38.37       119.08        29.10        84.20 
TCGA-04-1644 TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 
       48.89        31.86        29.16         9.47        17.98        35.57 
TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1670 TCGA-09-2049 TCGA-09-2050 
        9.99        38.43        61.87        17.98       112.41        71.11 
TCGA-09-2053 TCGA-09-2054 TCGA-10-0928 TCGA-10-0938 TCGA-13-0724 TCGA-13-0730 
       39.75        20.94        18.51        19.86         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        31.04        36.72        30.35        19.59 
TCGA-13-0802 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 
        8.19        91.40        74.27        66.67        70.39        67.99 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0916 TCGA-13-0920 
       48.33        47.84        44.94        44.84        21.17        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        4.64         6.41         6.08         6.05         5.92         6.84 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1487 TCGA-13-1489 TCGA-13-1492 TCGA-13-1497 
        4.21        87.06        22.39        82.88        73.55        54.31 
TCGA-13-1499 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 
       38.40         2.56         3.91         3.09        14.24        10.78 
TCGA-13-2065 TCGA-20-0991 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 
        8.75        26.20        19.10        16.70         2.66        47.54 
TCGA-23-1024 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 
       15.39        18.90         2.24        54.51         3.22        68.68 
TCGA-23-1119 TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-24-0968 TCGA-24-0970 
      129.96        39.09        58.13       115.89        19.66        11.64 
TCGA-24-0975 TCGA-24-1103 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1426 
       21.80        54.12         7.82         7.99         0.76         5.36 
TCGA-24-1430 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
       28.37        18.67         8.55        72.92        12.46         9.11 
TCGA-24-1545 TCGA-24-1548 TCGA-24-1550 TCGA-24-1553 TCGA-24-1564 TCGA-24-1614 
       57.40        16.21        41.06        58.09        25.87        48.33 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 
        8.32         3.48         3.72         3.81         4.37         5.52 
TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2026 TCGA-24-2027 
        9.80        30.21        11.05        81.11        34.82       109.71 
TCGA-24-2035 TCGA-24-2261 TCGA-24-2262 TCGA-24-2280 TCGA-24-2288 TCGA-24-2290 
       28.18         0.79         0.36        70.45         0.82        36.23 
TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1317 TCGA-25-1320 TCGA-25-1321 
       16.64        55.86         1.02         1.02        36.95        33.96 
TCGA-25-1323 TCGA-25-1627 TCGA-25-1632 TCGA-25-1633 TCGA-25-1870 TCGA-25-1871 
       12.00         0.36        56.94        60.59        14.96        24.99 
TCGA-25-1877 TCGA-25-2393 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 
       18.05        38.04        78.90        47.18       101.79         0.79 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1710 TCGA-29-1761 
       31.20        68.32         0.53        16.90        29.23        17.00 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1769 TCGA-29-1777 TCGA-29-1783 TCGA-29-1784 
       85.68        62.93        22.98        12.30         7.23         5.36 
TCGA-29-2429 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1862 TCGA-30-1887 
        4.90        38.07        51.91         2.47         6.12        24.26 
TCGA-31-1959 TCGA-36-1569 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 
        2.20        29.10         8.55        30.08        25.74        24.23 
TCGA-36-2530 TCGA-36-2534 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2552 
       33.01        29.82         2.24        18.31        20.52        11.47 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2593 TCGA-57-1582 TCGA-57-1992 
       26.04        23.74        42.02         1.48        24.03        29.00 
TCGA-59-2351 TCGA-59-2363 TCGA-61-1722 TCGA-61-1730 TCGA-61-1733 TCGA-61-1740 
      116.12         5.42         8.09         4.34        31.79         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1900 TCGA-61-1904 TCGA-61-1906 
       33.67        43.69         1.45         5.79         9.07        34.13 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 
       56.61        43.43        15.75        38.17         5.52        14.50 
TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 
       17.98        30.64         1.18        65.52         6.48        76.87 
TCGA-61-2109 TCGA-61-2113 
       20.68        22.22 

$`DEL PEAK  6(3P26.2) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81         2.01        46.62        18.51        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 
       48.76        21.57        63.98        32.52        44.32        33.67 
TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1638 TCGA-04-1646 
       71.47        56.55        41.59        19.99        55.43        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 
       28.64        64.64        36.23        47.70        45.37        57.76 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
       89.33        74.93        41.62        57.60        55.36        30.51 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 
       35.15         4.54        63.09        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       25.91        81.47        33.24        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.44        35.80        15.12         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 
       39.58        12.39        31.10        15.19         2.50        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        34.06        32.25        21.40         8.45        38.93 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 
       28.70         8.71         7.79         8.12         8.28        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0889 
       35.28        35.28        13.61        68.94       107.18        61.84 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       69.01        43.36        57.47        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 
       47.38        37.08        27.72        34.06        29.98        14.89 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 
       10.88         6.61         7.36         4.70         5.33        54.64 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 
       61.71        29.42        98.04        20.68        70.82        52.44 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 
       38.20        49.25         4.24        37.61        13.97        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-2059 
       16.57         4.21         4.41         4.77         4.18        12.23 
TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.61         6.28        54.77         8.42        23.05        25.94 
TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 TCGA-20-1686 TCGA-23-1022 TCGA-23-1023 
       72.20        27.52        25.38         2.93        42.54        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1109 
       26.83        31.76        49.41         8.81        29.13        51.35 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 
       31.20         4.57        33.30        86.01         4.27         6.38 
TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       33.47         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-24-0979 
       49.84         2.76         4.70         4.50         7.63        41.56 
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-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 
        7.86         6.25         6.02         5.95         4.83        17.39 
TCGA-24-1431 TCGA-24-1435 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 
       19.17        43.53        45.14       105.99         3.45         1.18 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 
       22.22        26.96        64.27        56.58        51.91        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-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 
       47.70        10.26        17.23        90.15        88.37        38.24 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 
       11.28         5.79        22.68        16.44         4.87       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 
       44.84        58.16        14.43        53.95        18.48        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 
       44.52        57.07        36.16        47.54        31.63        44.61 
TCGA-24-2289 TCGA-24-2295 TCGA-24-2298 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       67.36        33.11        53.26        26.96        32.02        51.06 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1319 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 
       37.02        34.98        65.00         2.99         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1634 
       18.02        15.81        20.61         7.86         0.30        35.54 
TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 
       51.22        85.05        13.02        49.05         1.02         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-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 TCGA-29-1702 
       31.00        26.99        44.71        38.53        33.70        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1763 TCGA-29-1766 
       59.67        18.25        41.98        34.62        66.81        39.12 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       31.23        24.36        22.55        17.33        12.36        11.84 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       14.93         8.38        34.62        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
       45.11        42.25        11.84        11.47         9.76        21.04 
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-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 
       36.62         1.22        57.57        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-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1578 TCGA-36-1581 
       28.77        21.53        22.85        22.55        27.85        24.69 
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-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2588 
       20.98        14.17         6.05        16.18         7.99         9.44 
TCGA-42-2590 TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        7.46        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-59-A5PD TCGA-61-1721 TCGA-61-1724 
       34.39         2.14        44.81        20.52        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-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 
       35.80         8.42        11.41        13.02        31.30        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1915 TCGA-61-1995 TCGA-61-2003 TCGA-61-2008 
       42.51        48.92        67.76         2.01         4.01        30.64 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 
       39.85        45.96        45.40         4.80         4.77        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2110 
       71.74        61.64        58.39        60.62        55.50        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-VG-A8LO TCGA-WR-A838 
        0.79         8.05 

  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 
                       129.96                        180.20 
  DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE 
                       24.130                        29.455 
[1] "0.4 - 130.0 (24.1)" "0.3 - 180.2 (29.5)"
[1] "hr=" "1"  
D39V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  6(3P26.2) MUTATED         2   200                0
  DEL PEAK  6(3P26.2) WILD-TYPE       0   357                2
D39V3, multiclass
                  clus
vv                 DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    200                           357
  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, continuous
D39V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.2) MUTATED     3 203
  DEL PEAK  6(3P26.2) WILD-TYPE   0 365
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED      3  203
  DEL PEAK  6(3P26.2) WILD-TYPE    0  365
     clus
vv    DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  NO                            3                             0
  YES                         203                           365
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  6(3P26.2) MUTATED    6  6  1  0
  DEL PEAK  6(3P26.2) WILD-TYPE  8 20  4  3
D39V6, multiclass
    clus
vv   DEL PEAK  6(3P26.2) MUTATED DEL PEAK  6(3P26.2) WILD-TYPE
  R0                           6                             8
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P26.2) MUTATED                                  1     6
  DEL PEAK  6(3P26.2) WILD-TYPE                                2    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(3P26.2) MUTATED                           8
  DEL PEAK  6(3P26.2) WILD-TYPE                        24
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(3P26.2) MUTATED                                           1   174
  DEL PEAK  6(3P26.2) WILD-TYPE                                         0   301
D39V7, multiclass
                                           clus
vv                                          DEL PEAK  6(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               6
  BLACK OR AFRICAN AMERICAN                                           8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             174
                                           clus
vv                                          DEL PEAK  6(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                12
  BLACK OR AFRICAN AMERICAN                                            24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               301
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.2) MUTATED     3 110
  DEL PEAK  6(3P26.2) WILD-TYPE   7 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.2) MUTATED      3  110
  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                         110
                        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    39  43
  DEL PEAK  7(3Q13.31) WILD-TYPE 227 247
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            82                            474 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            43                            247 
$`DEL PEAK  7(3Q13.31) MUTATED`
TCGA-04-1356 TCGA-04-1514 TCGA-04-1651 TCGA-04-1652 TCGA-09-0369 TCGA-09-2050 
       49.28        56.55        36.23        31.86        35.57        71.11 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0720 TCGA-13-0751 TCGA-13-0762 TCGA-13-0791 
       35.80        19.86        44.55        55.17        32.25        38.93 
TCGA-13-0794 TCGA-13-0803 TCGA-13-0807 TCGA-13-0887 TCGA-13-0889 TCGA-13-0906 
       30.35        43.86        13.61        66.67        61.84        44.94 
TCGA-13-0910 TCGA-13-0920 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
       37.08        13.81         7.36         5.92         4.70         4.21 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1492 TCGA-13-1507 TCGA-13-1512 TCGA-20-1684 
       22.39        70.82        73.55         4.77         3.09        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1024 TCGA-23-1027 TCGA-23-1032 TCGA-23-1118 
       16.70         2.66        15.39        31.76         2.24        86.01 
TCGA-23-1121 TCGA-24-0970 TCGA-24-1418 TCGA-24-1422 TCGA-24-1426 TCGA-24-1436 
        6.38        11.64         7.99         0.76         5.36         8.55 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1471 TCGA-24-1545 TCGA-24-1927 
       12.46        45.14         9.11         1.18        57.40        16.44 
TCGA-24-2020 TCGA-25-1317 TCGA-25-1318 TCGA-25-1321 TCGA-25-1623 TCGA-25-1626 
      152.02         1.02        34.98        33.96        18.58        15.81 
TCGA-25-2393 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1710 TCGA-29-1777 
       38.04        38.53         0.79        31.20        29.23        12.30 
TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-36-1568 TCGA-36-1578 TCGA-36-2540 
        7.23        65.00        45.11        28.77        27.85        23.80 
TCGA-42-2587 TCGA-42-2589 TCGA-59-2350 TCGA-59-2354 TCGA-61-1724 TCGA-61-1730 
       23.74        42.02        22.32        34.39        20.94         4.34 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1904 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 
       33.67        43.69         9.07        38.17         4.01        30.64 
TCGA-61-2018 TCGA-61-2096 TCGA-61-2101 TCGA-61-2613 
       45.40        58.39        55.50        31.07 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       18.51        11.87        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98        65.46        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       71.47        82.39        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-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       64.64        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       17.98         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
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-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        63.09        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 
       32.28        11.70         3.91        35.44        15.12         6.21 
TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 
       24.59        39.58         2.73        12.39        31.10        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       17.82         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       31.04        21.40         8.45        36.72        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
        8.71         7.79         8.12         8.28         8.19        35.28 
TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.28        68.94       107.18        91.40        74.27        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       67.99        69.01        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 
       19.36        47.38        48.33        47.84        44.84        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 
       34.06        29.98        21.17        14.89         4.64         6.41 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1409 TCGA-13-1412 
        6.08        10.88         6.61         6.05         6.84         5.33 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 
       54.64        87.06        61.71        29.42        98.04        20.68 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       82.88        52.44        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 
        4.41         4.18         2.56         3.91        14.24        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1028 
        2.93        47.54        42.54        40.54        26.83        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
        8.81        29.13        18.90        51.35        54.51         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1120 
       31.20        68.68         4.57        33.30       129.96         4.27 
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-23-2079 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-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 
        4.50         7.63        19.66        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        19.17        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        53.95        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 
       32.02        51.06        37.02        65.00        36.95         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.00         2.96        18.02         0.36        20.61         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        18.05        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        44.71        47.18 
TCGA-29-1693 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
      101.79        33.70        68.32         0.53        16.90        18.67 
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        17.00        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.12        31.23        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        34.62        86.17        62.47         4.90        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       11.84        11.47         9.76        21.04        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-3P-A9WA TCGA-42-2582 
       14.17         6.05        16.18        11.47         7.99        26.04 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        9.44         7.46        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 
       21.14         1.74        22.32        29.00        25.08        25.02 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
      180.20        80.12       116.12         9.40         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 
       44.81        20.52        11.11         8.09        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       27.88        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
        2.43         1.45         8.42         5.79        11.41        13.02 
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-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 
       67.76        43.43        15.75         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 
       17.98        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-61-2102 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-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35         8.61        39.68        18.94         0.79         8.05 

  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 
                         29.79                          27.80 
[1] "0.8 - 152.0 (29.8)" "0.3 - 180.2 (27.8)"
[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       2   475                2
D40V3, multiclass
                  clus
vv                 DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                      82                            475
  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, continuous
D40V5, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     0  84
  DEL PEAK  7(3Q13.31) WILD-TYPE   3 484
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      0   84
  DEL PEAK  7(3Q13.31) WILD-TYPE    3  484
     clus
vv    DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  NO                             0                              3
  YES                           84                            484
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  7(3Q13.31) MUTATED    1  6  0  0
  DEL PEAK  7(3Q13.31) WILD-TYPE 13 20  5  3
D40V6, multiclass
    clus
vv   DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  R0                            1                             13
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q13.31) MUTATED                                  0     2
  DEL PEAK  7(3Q13.31) WILD-TYPE                                3    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(3Q13.31) MUTATED                           3
  DEL PEAK  7(3Q13.31) WILD-TYPE                        29
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  7(3Q13.31) MUTATED                                           0
  DEL PEAK  7(3Q13.31) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK  7(3Q13.31) MUTATED      74
  DEL PEAK  7(3Q13.31) WILD-TYPE   401
D40V7, multiclass
                                           clus
vv                                          DEL PEAK  7(3Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               74
                                           clus
vv                                          DEL PEAK  7(3Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                401
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     1  54
  DEL PEAK  7(3Q13.31) WILD-TYPE   9 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      1   54
  DEL PEAK  7(3Q13.31) WILD-TYPE    9  271
                        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                            271
[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   181 194
  DEL PEAK  8(4Q22.1) WILD-TYPE  85  96
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          375                           181 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                          194                            96 
$`DEL PEAK  8(4Q22.1) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1343 TCGA-04-1348 TCGA-04-1350 
       40.24        41.00        49.15        11.87        48.76        63.98 
TCGA-04-1361 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       32.52        33.67        71.47        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       19.99       119.08        29.10        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       27.88        28.64        64.64        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       45.37        29.16        57.76        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 
       38.43        89.33        74.93        57.60        55.36        30.51 
TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 
       17.98         8.55        97.55         6.12       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 
       63.09        39.75        20.94        26.93        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0935 TCGA-10-0937 TCGA-13-0717 
       81.47        18.51        33.24        35.44        15.12        24.59 
TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 
       44.55         2.73        12.39        15.19        17.82        55.17 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0792 TCGA-13-0793 
       11.18        11.38        11.54        32.25        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 
       30.35        19.59         8.71         8.28        43.86        35.28 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 
       68.94       107.18        91.40        66.67        70.39        61.84 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       67.99        56.15        47.38        47.84        44.94        37.08 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
        4.64         6.41         6.08        10.88         6.61         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 TCGA-13-1487 
        5.92         6.84         4.70        87.06        98.04        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       54.31        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 
        4.18         2.56         3.91         3.09        14.24        12.23 
TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1682 TCGA-20-1683 
       10.78         8.75        54.77        25.94        27.52        25.38 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1028 
       19.10         2.93         2.66        47.54        42.54        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
        8.81        29.13         2.24        54.51         3.22        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
       68.68         4.57        86.01       129.96        39.09        33.47 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 
       58.13         0.53        24.95        87.48        49.84         2.76 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0982 
        4.70         4.50        19.66        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        19.17        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        53.95        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        32.02 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       37.02         1.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       12.00         2.96        18.02        15.81         0.36        20.61 
TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        7.86         0.30        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2398 
       24.99        18.05        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        47.18 
TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1705 TCGA-29-1762 
        0.79        31.20        68.32         0.53        18.25        85.68 
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-3P-A9WA 
        2.24        20.52        14.17        16.18        11.47         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
       26.04        23.74         9.44        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
        1.48        24.03        21.14         1.74        29.00        25.08 
TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
      180.20        22.32       116.12         9.40         2.14         5.42 
TCGA-59-2372 TCGA-61-1725 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 
       44.81        31.43         4.34        31.79        28.47        48.79 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 TCGA-61-1895 TCGA-61-1899 
       44.84        35.80         2.43        33.67         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
        5.79        11.41        13.02         9.07        34.13        31.30 
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-61-2018 TCGA-61-2092 TCGA-61-2094 
       30.64        39.85         1.18        45.40        51.72        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-61-2110 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-VG-A8LO 
       39.68        18.94         0.79 

$`DEL PEAK  8(4Q22.1) WILD-TYPE`
TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 
        1.81         2.01        46.62        18.51        65.52        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 TCGA-04-1365 TCGA-04-1525 
       21.57        65.46        49.28        44.32        76.57        38.37 
TCGA-09-0365 TCGA-09-1665 TCGA-09-1667 TCGA-09-1672 TCGA-09-1673 TCGA-09-2043 
        9.47        41.62        61.87         5.85         3.02         6.18 
TCGA-09-2045 TCGA-09-2048 TCGA-10-0925 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       35.15         4.54        54.31        32.28        11.70         3.91 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0723 TCGA-13-0726 TCGA-13-0755 
       35.80        19.86         6.21        39.58        31.10         2.50 
TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0799 
       34.06        31.04        21.40         8.45        38.93         7.79 
TCGA-13-0800 TCGA-13-0802 TCGA-13-0805 TCGA-13-0807 TCGA-13-0886 TCGA-13-0891 
        8.12         8.19        35.28        13.61        74.27        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0908 
       43.36        57.47        57.07        19.36        48.33        44.84 
TCGA-13-1405 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 
        7.36         4.21         5.33        54.64        61.71        29.42 
TCGA-13-1485 TCGA-13-1496 TCGA-13-1498 TCGA-13-1506 TCGA-13-1507 TCGA-13-2060 
       20.68         4.24        37.61         4.41         4.77         8.61 
TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1685 
        6.28         8.42        23.05        26.20        72.20        16.70 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1031 TCGA-23-1109 
       40.54        15.39        26.83        31.76        18.90        51.35 
TCGA-23-1117 TCGA-23-1120 TCGA-23-1121 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 
       33.30         4.27         6.38       115.89        91.66        77.00 
TCGA-24-0966 TCGA-24-0979 TCGA-24-0980 TCGA-24-1423 TCGA-24-1427 TCGA-24-1464 
        7.63        41.56         7.66         6.25         4.83        12.46 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1546 TCGA-24-1549 TCGA-24-1550 
       45.14       105.99         9.11        64.27        56.58        41.06 
TCGA-24-1553 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1843 TCGA-24-1845 
       58.09        25.87        10.26        88.37         3.48         3.81 
TCGA-24-2026 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
       34.82        18.48        28.18        64.01        44.52         0.36 
TCGA-24-2289 TCGA-25-1313 TCGA-25-1315 TCGA-25-1319 TCGA-25-1623 TCGA-25-1632 
       67.36        26.96        51.06        65.00        18.58        56.94 
TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 
       85.05        38.04         3.02        12.00        19.99         2.96 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 
       44.71       101.79        38.53        33.70        16.90        18.67 
TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1766 
       59.67        41.98        29.23        34.62        17.00        39.12 
TCGA-29-1768 TCGA-29-1774 TCGA-29-1775 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       31.23        17.33        12.36        34.62        62.47         4.90 
TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1857 TCGA-30-1859 
       11.84         9.76        21.04        51.91         0.26        48.10 
TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 
        6.12        36.62         1.22        24.26        48.79        45.57 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-1578 
       22.49        44.12        28.77        29.10        22.55        27.85 
TCGA-36-2537 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 TCGA-36-2549 TCGA-57-1583 
       25.91        23.80        20.98        18.31         6.05        11.38 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2349 TCGA-59-2354 TCGA-59-A5PD TCGA-61-1721 
       22.32        25.02        80.12        34.39        20.52        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1743 TCGA-61-1910 
        8.09        20.94        18.54        27.88        43.69        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
       42.51        48.92        56.61        67.76        15.75        38.17 
TCGA-61-2012 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 
       30.64        45.96         4.80         4.77        61.64        58.39 
TCGA-WR-A838 
        8.05 

  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                        115.89 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                        28.37                         27.88 
[1] "0.3 - 180.2 (28.4)" "0.3 - 115.9 (27.9)"
[1] "hr=" "1.1"
D41V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  8(4Q22.1) MUTATED         2   376                1
  DEL PEAK  8(4Q22.1) WILD-TYPE       0   181                1
D41V3, multiclass
                  clus
vv                 DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    376                           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, continuous
D41V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.1) MUTATED     2 387
  DEL PEAK  8(4Q22.1) WILD-TYPE   1 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      2  387
  DEL PEAK  8(4Q22.1) WILD-TYPE    1  181
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NO                            2                             1
  YES                         387                           181
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(4Q22.1) MUTATED   11 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                          11                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4Q22.1) MUTATED                                  3    11
  DEL PEAK  8(4Q22.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(4Q22.1) MUTATED                          22
  DEL PEAK  8(4Q22.1) WILD-TYPE                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4Q22.1) MUTATED                                           1   322
  DEL PEAK  8(4Q22.1) WILD-TYPE                                         0   153
D41V7, multiclass
                                           clus
vv                                          DEL PEAK  8(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             322
                                           clus
vv                                          DEL PEAK  8(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               153
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4Q22.1) MUTATED     9 212
  DEL PEAK  8(4Q22.1) WILD-TYPE   1 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      9  212
  DEL PEAK  8(4Q22.1) WILD-TYPE    1  113
                        clus
vv                       DEL PEAK  8(4Q22.1) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         212
                        clus
vv                       DEL PEAK  8(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           113
[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   192 211
  DEL PEAK  9(4Q34.3) WILD-TYPE  74  79
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          403                           153 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          211                            79 
$`DEL PEAK  9(4Q34.3) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 
       40.24        41.00         1.81        49.15        46.62        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        48.76        63.98        65.46        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       44.32        33.67        71.47        82.39        56.55        41.59 
TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 
       19.99        29.10        84.20        55.43        48.89        27.88 
TCGA-04-1649 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        31.86        47.70        45.37        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         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-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       25.91        81.47        18.51        33.24        32.28        11.70 
TCGA-10-0935 TCGA-10-0937 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 
       35.44        15.12         6.21        24.59        44.55         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-13-0766 TCGA-13-0792 TCGA-13-0793 
       11.54        34.06        32.25        21.40        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       30.35        19.59         8.71         8.12         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        35.28        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0890 TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       66.67        67.99        56.15        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 
       21.17        14.89        13.81         4.64         6.41        10.88 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 
        6.61         6.05         5.92         6.84         5.33        87.06 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 
       73.55        49.25        54.31        38.40        13.97        16.57 
TCGA-13-1505 TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 
        4.21         4.18         3.09        14.24        12.23        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0990 TCGA-20-1683 TCGA-20-1685 
        8.75         6.28        54.77        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        42.54        26.83        31.76 
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         2.24        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         4.57        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 
       19.17        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        53.95 
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        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       34.98        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
       18.02        15.81         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-2042 
       56.94        60.59        35.54        51.22        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        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32         0.53        16.90        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 
       29.23        34.62        17.00        85.68        62.93        31.23 
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         4.90        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-3P-A9WA TCGA-42-2587 
       14.17         6.05        16.18        11.47         7.99        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2350 
       21.14         1.74        29.00        25.08        25.02        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-59-A5PD TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.52        18.54        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1899 TCGA-61-1900 
       48.79        44.84         2.43        33.67         8.42         5.79 
TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
       13.02         9.07        34.13        31.30        37.05        42.51 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 TCGA-61-2003 TCGA-61-2008 
       56.61        43.43        15.75         2.01         4.01        30.64 
TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2092 TCGA-61-2094 
       39.85        30.64         1.18        45.40        51.72        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-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56Q 
       44.52       125.75        22.22         6.35         8.61        18.94 
TCGA-VG-A8LO 
        0.79 

$`DEL PEAK  9(4Q34.3) WILD-TYPE`
TCGA-04-1337 TCGA-04-1342 TCGA-04-1349 TCGA-04-1361 TCGA-04-1365 TCGA-04-1525 
        2.01        18.51        21.57        32.52        76.57        38.37 
TCGA-04-1530 TCGA-04-1648 TCGA-04-1651 TCGA-09-0365 TCGA-09-1667 TCGA-09-1668 
      119.08        28.64        36.23         9.47        61.87        55.36 
TCGA-09-1672 TCGA-10-0925 TCGA-10-0934 TCGA-10-0936 TCGA-10-0938 TCGA-13-0723 
        5.85        54.31         3.91        35.80        19.86        39.58 
TCGA-13-0726 TCGA-13-0755 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 TCGA-13-0799 
       31.10         2.50        31.04         8.45        38.93         7.79 
TCGA-13-0807 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       13.61        74.27        70.39        61.84        69.01        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0924 TCGA-13-1405 TCGA-13-1410 
       57.47        57.07        19.36         6.08         7.36         4.70 
TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1494 TCGA-13-1496 
        4.21        54.64        61.71        20.68        38.20         4.24 
TCGA-13-1498 TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 TCGA-13-1511 
       37.61        32.84         4.41         4.77         2.56         3.91 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.61         8.42        23.05        26.20        72.20        27.52 
TCGA-20-1684 TCGA-23-1023 TCGA-23-1024 TCGA-23-1123 TCGA-23-2078 TCGA-23-2645 
       19.10        40.54        15.39        33.47        87.48         4.50 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-1104 TCGA-24-1417 TCGA-24-1424 
        7.63        19.66        21.80        63.55         7.82         6.02 
TCGA-24-1427 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1467 TCGA-24-1549 
        4.83        43.53        72.92        12.46       105.99        56.58 
TCGA-24-1553 TCGA-24-1558 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1614 
       58.09        19.53        45.50        25.87        10.26        48.33 
TCGA-24-1616 TCGA-24-1847 TCGA-24-1927 TCGA-24-2019 TCGA-24-2033 TCGA-24-2035 
       38.24        11.28        16.44         4.87        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2288 TCGA-24-2297 TCGA-25-1319 
       64.01        44.52         0.36         0.82        55.86        65.00 
TCGA-25-1320 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2396 
       36.95        14.96        18.05        85.05        38.04         3.02 
TCGA-25-2399 TCGA-25-2401 TCGA-25-2409 TCGA-29-1690 TCGA-29-1691 TCGA-29-1702 
       19.99         2.96        26.99        44.71        47.18        18.67 
TCGA-29-1703 TCGA-29-1763 TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 
       59.67        66.81        39.12        24.36        17.33        12.36 
TCGA-29-1778 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2432 TCGA-29-2436 
       14.93        34.62        86.17        62.47        11.84         9.76 
TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1862 TCGA-30-1887 TCGA-30-1892 TCGA-31-1951 
       21.04         2.47         6.12        24.26        48.79        22.49 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-2534 TCGA-36-2540 
       44.12        28.77        29.10        22.55        29.82        23.80 
TCGA-42-2582 TCGA-57-1583 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-61-1721 
       26.04        11.38        22.32       180.20        80.12        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1738 TCGA-61-1743 TCGA-61-1895 
        8.09        20.94        31.43        35.80        43.69         1.45 
TCGA-61-1901 TCGA-61-1913 TCGA-61-1915 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 
       11.41        48.92        67.76        38.17         5.52        14.50 
TCGA-61-2002 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2095 TCGA-61-2096 
       17.98        45.96         4.80         4.77        61.64        58.39 
TCGA-61-2613 TCGA-OY-A56P TCGA-WR-A838 
       31.07        39.68         8.05 

  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 
                        29.00                         26.04 
[1] "0.3 - 152.0 (29.0)" "0.4 - 180.2 (26.0)"
[1] "hr=" "1"  
D42V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK  9(4Q34.3) MUTATED         2   404                1
  DEL PEAK  9(4Q34.3) WILD-TYPE       0   153                1
D42V3, multiclass
                  clus
vv                 DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    404                           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, continuous
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED     3 412
  DEL PEAK  9(4Q34.3) WILD-TYPE   0 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED      3  412
  DEL PEAK  9(4Q34.3) WILD-TYPE    0  156
     clus
vv    DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  NO                            3                             0
  YES                         412                           156
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  9(4Q34.3) MUTATED   12 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                          12                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4Q34.3) MUTATED                                  3    13
  DEL PEAK  9(4Q34.3) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(4Q34.3) MUTATED                          22
  DEL PEAK  9(4Q34.3) WILD-TYPE                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(4Q34.3) MUTATED                                           1   341
  DEL PEAK  9(4Q34.3) WILD-TYPE                                         0   134
D42V7, multiclass
                                           clus
vv                                          DEL PEAK  9(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             341
                                           clus
vv                                          DEL PEAK  9(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    10 233
  DEL PEAK  9(4Q34.3) WILD-TYPE   0  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     10  233
  DEL PEAK  9(4Q34.3) WILD-TYPE    0   92
                        clus
vv                       DEL PEAK  9(4Q34.3) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         233
                        clus
vv                       DEL PEAK  9(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            92
[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   162 177
  DEL PEAK 10(5Q12.1) WILD-TYPE 104 113
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          339                           217 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          177                           113 
$`DEL PEAK 10(5Q12.1) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1347 
       40.24        41.00         1.81        49.15        18.51        63.09 
TCGA-04-1349 TCGA-04-1351 TCGA-04-1362 TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 
       21.57        65.46        44.32        19.99        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-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 
       47.70        29.16         9.47        57.76        35.57        38.43 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1674 
       89.33        41.62        61.87        55.36        30.51         8.55 
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-09-2054 TCGA-10-0925 TCGA-10-0927 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 
       20.94        54.31        81.47        32.28        11.70         3.91 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 
       35.44        15.12        19.86        24.59        39.58         2.73 
TCGA-13-0725 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 
       12.39        17.82        55.17        11.18        11.54        34.06 
TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 
       32.25        31.04        21.40        36.72        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       35.28        35.28       107.18        91.40        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 
       61.84        67.99        69.01        43.36        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0911 TCGA-13-0916 
       47.38        48.33        47.84        44.94        27.72        21.17 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 
       13.81         4.64         6.41         6.08        10.88         6.61 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 
        7.36         6.05         5.92         6.84         4.21         5.33 
TCGA-13-1482 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 
       61.71        98.04        70.82        82.88        52.44        73.55 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 
        4.24        54.31        32.84        16.57         4.21         4.18 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 
        2.56         3.09        14.24        12.23         8.61         8.75 
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-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.93         2.66        47.54        40.54        15.39        26.83 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1113 
       49.41         8.81        18.90         2.24        54.51        31.20 
TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
       68.68         4.57        33.30       129.96        39.09        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 
       58.13        24.95       115.89        77.00        49.84         4.70 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1104 
        4.50        11.64        41.56         7.66        22.32        63.55 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1425 TCGA-24-1427 
       47.41         7.82         7.99         7.86         5.95         4.83 
TCGA-24-1428 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 
       17.39        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1546 TCGA-24-1548 
       12.46        45.14         9.11         3.45        64.27        16.21 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 TCGA-24-1553 TCGA-24-1558 TCGA-24-1564 
       56.58        41.06        41.39        58.09        19.53        25.87 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1847 
       17.23        88.37        48.33        38.24         8.32        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-24-2026 
       11.05        81.11         4.87       152.02        44.84        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 
      109.71        14.43        53.95        18.48        28.18        57.07 
TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 
       36.16         0.79        47.54        31.63        70.45        44.61 
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-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       32.02         1.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1626 TCGA-25-1627 TCGA-25-1633 TCGA-25-1634 
       12.00         2.96        15.81         0.36        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2392 
       51.22        14.96        24.99        18.05        49.05         1.02 
TCGA-25-2393 TCGA-25-2398 TCGA-25-2400 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 
       38.04        45.01        42.02        29.03        78.90        47.18 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 
       38.53         0.79        33.70        31.20        68.32        16.90 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 
       18.67        18.25        41.98        29.23        17.00        85.68 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1775 TCGA-29-1777 
       62.93        39.12        31.23        22.98        12.36        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
       14.93         7.23        86.17        65.00        62.47        45.11 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 
       42.25        11.84        11.47        21.04        51.91         2.47 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 
        0.26        48.10        34.78        36.62         1.22        24.26 
TCGA-30-1891 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1575 
       30.05        30.18         6.71        42.51         2.20         8.55 
TCGA-36-1576 TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2538 
       30.08        27.85        24.69        33.01        29.82        25.08 
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-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
       16.18        11.47         7.99        23.74        42.02         7.46 
TCGA-42-2591 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2348 
       40.77        11.38        21.14         1.74        29.00       180.20 
TCGA-59-2351 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
      116.12        20.52         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 
       27.88        31.79        44.84         2.43        33.67        43.69 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 
        1.45         8.42        11.41        13.02        34.13        31.30 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-2003 
       48.92        56.61        43.43        15.75        38.17         4.01 
TCGA-61-2012 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 
       30.64        45.40         4.77        71.74        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-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

$`DEL PEAK 10(5Q12.1) WILD-TYPE`
TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 
        2.01        46.62        11.87        65.52        48.76        63.98 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 
       49.28        32.52        33.67        76.57        71.47        82.39 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1644 TCGA-04-1652 TCGA-04-1655 
       56.55        41.59       119.08        48.89        31.86        45.37 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1670 TCGA-09-1672 
       17.98         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-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0936 TCGA-13-0714 TCGA-13-0720 
       25.91        18.51        33.24        35.80         6.21        44.55 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 TCGA-13-0768 TCGA-13-0791 
       31.10        15.19         2.50        11.38         8.45        38.93 
TCGA-13-0794 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 TCGA-13-0897 TCGA-13-0899 
       30.35        13.61        68.94        74.27        57.47        56.15 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0912 TCGA-13-0913 TCGA-13-0919 TCGA-13-1410 
       44.84        37.08        34.06        29.98        14.89         4.70 
TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1487 TCGA-13-1494 
       54.64        87.06        29.42        20.68        22.39        38.20 
TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1506 TCGA-13-1507 
       49.25        37.61        38.40        13.97         4.41         4.77 
TCGA-13-1511 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        3.91        10.78         6.28        54.77         8.42        23.05 
TCGA-20-0996 TCGA-23-1022 TCGA-23-1027 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 
       72.20        42.54        31.76        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-24-0968 TCGA-24-0975 TCGA-24-1103 TCGA-24-1413 
        2.76         7.63        19.66        21.80        54.12         6.31 
TCGA-24-1416 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 
        6.38         0.76         6.25         6.02         5.36        28.37 
TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1551 
      105.99         1.18        22.22        26.96        57.40        51.91 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       88.50        70.62        39.88        44.09        45.50        47.70 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       10.26        90.15         3.48         3.72         3.81         4.37 
TCGA-24-2024 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2289 TCGA-24-2295 
       58.16        64.01        44.52         0.36        67.36        33.11 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1623 TCGA-25-1625 
       26.96        51.06        37.02        65.00        18.58        18.02 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1878 TCGA-25-2042 
       20.61         7.86         0.30        56.94        85.05        13.02 
TCGA-25-2396 TCGA-25-2397 TCGA-25-2399 TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 
        3.02        12.00        19.99         2.96        31.00        26.99 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1699 TCGA-29-1703 TCGA-29-1711 TCGA-29-1763 
       44.71       101.79         0.53        59.67        34.62        66.81 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 TCGA-29-1784 
       24.36        22.55        17.33        11.84         8.38         5.36 
TCGA-29-1785 TCGA-29-2429 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 
       34.62         4.90         9.76        38.07        36.26        15.68 
TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 
       44.91         6.12        57.57        48.79        45.57        18.77 
TCGA-31-1951 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 
       22.49        44.12        28.77        29.10        21.53        22.85 
TCGA-36-1574 TCGA-36-1577 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 
       22.55        25.74        24.23        35.05        29.49        25.91 
TCGA-36-2540 TCGA-36-2548 TCGA-42-2582 TCGA-42-2588 TCGA-42-2593 TCGA-57-1582 
       23.80        14.17        26.04         9.44         1.48        24.03 
TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 
       22.32        25.08        25.02        80.12        22.32         9.40 
TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1730 
       34.39         2.14         5.42        44.81        11.11         4.34 
TCGA-61-1734 TCGA-61-1736 TCGA-61-1738 TCGA-61-1900 TCGA-61-1904 TCGA-61-1910 
       28.47        48.79        35.80         5.79         9.07        37.05 
TCGA-61-1911 TCGA-61-1915 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       42.51        67.76         2.01         5.52        14.50        17.98 
TCGA-61-2008 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       30.64        39.85         1.18        45.96         4.80        51.72 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 
       61.64        58.39        44.52         6.35        31.07         8.61 
TCGA-OY-A56P 
       39.68 

  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                        119.08 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                        28.18                         26.99 
[1] "0.3 - 180.2 (28.2)" "0.3 - 119.1 (27.0)"
[1] "hr=" "1"  
D43V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 10(5Q12.1) MUTATED         2   340                1
  DEL PEAK 10(5Q12.1) WILD-TYPE       0   217                1
D43V3, multiclass
                  clus
vv                 DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    340                           217
  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, continuous
D43V5, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED     1 348
  DEL PEAK 10(5Q12.1) WILD-TYPE   2 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      1  348
  DEL PEAK 10(5Q12.1) WILD-TYPE    2  220
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  NO                            1                             2
  YES                         348                           220
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 10(5Q12.1) MUTATED    7 16  1  2
  DEL PEAK 10(5Q12.1) WILD-TYPE  7 10  4  1
D43V6, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  R0                           7                             7
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5Q12.1) MUTATED                                  1    13
  DEL PEAK 10(5Q12.1) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(5Q12.1) MUTATED                          15
  DEL PEAK 10(5Q12.1) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(5Q12.1) MUTATED                                           0   294
  DEL PEAK 10(5Q12.1) WILD-TYPE                                         1   181
D43V7, multiclass
                                           clus
vv                                          DEL PEAK 10(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             294
                                           clus
vv                                          DEL PEAK 10(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               181
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED     6 197
  DEL PEAK 10(5Q12.1) WILD-TYPE   4 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      6  197
  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                         197
                        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   200 201
  DEL PEAK 11(5Q13.2) WILD-TYPE  66  89
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          401                           155 
  DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE 
                          201                            89 
$`DEL PEAK 11(5Q13.2) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 
       63.09        21.57        63.98        65.46        49.28        32.52 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1542 
       76.57        71.47        41.59        19.99        29.10        84.20 
TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       48.89        27.88        28.64        64.64        36.23        47.70 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 
       29.16         9.47        57.76        17.98        35.57        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-10-0925 TCGA-10-0927 TCGA-10-0928 
       71.11        20.94        26.93        54.31        81.47        18.51 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 
       32.28        11.70         3.91        35.44        15.12        19.86 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 
       24.59        44.55        39.58         2.73        12.39        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       55.17        11.18        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
       21.40        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        7.79         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       35.28       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       61.84        67.99        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       57.07        19.36        47.38        48.33        47.84        44.94 
TCGA-13-0908 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       44.84        27.72        29.98        21.17        14.89        13.81 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
        4.64         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 
        6.05         5.92         6.84         4.70         4.21         5.33 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 
       87.06        61.71        29.42        98.04        70.82        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 
       52.44        73.55         4.24        54.31        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
       16.57         4.21         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT 
       12.23         8.61        10.78         8.75         6.28        54.77 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       25.94        26.20        27.52        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
        2.66        47.54        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 
       31.76        49.41         8.81        18.90         2.24        51.35 
TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
       54.51        31.20        68.68         4.57        33.30        86.01 
TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 
      129.96        39.09        33.47        58.13        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-24-0970 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-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1423 
       63.55         7.82         7.99         7.86         0.76         6.25 
TCGA-24-1424 TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 
        6.02         5.95         4.83        17.39        28.37        19.17 
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-24-1470 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 
        3.45        64.27        16.21        56.58        41.06        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-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       88.37        48.33        38.24         8.32         3.48         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-24-1924 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-24-2023 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        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       18.48        28.18        57.07        36.16         0.79        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-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       32.02         1.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       12.00        18.02        15.81         0.36         7.86         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        49.05         1.02         3.02        12.00        45.01 
TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 TCGA-29-1688 TCGA-29-1691 
       42.02         2.96        29.03        26.99        78.90        47.18 
TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 
       38.53         0.79        33.70        31.20        16.90        18.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 
       18.25        41.98        29.23        34.62        17.00        85.68 
TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       66.81        62.93        39.12        31.23        22.98        24.36 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2431 
        5.36        86.17        65.00        62.47        45.11        42.25 
TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1718 TCGA-30-1855 TCGA-30-1857 
       11.84        11.47        21.04        51.91         2.47         0.26 
TCGA-30-1859 TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 
       48.10        34.78        36.62         1.22        24.26        30.05 
TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1569 
       30.18         6.71        42.51        44.12         2.20        29.10 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1581 TCGA-36-2530 TCGA-36-2534 TCGA-36-2538 
        8.55        30.08        24.69        33.01        29.82        25.08 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2549 TCGA-36-2552 
       21.60        20.98        18.31        20.52         6.05        11.47 
TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 
        7.99        23.74        42.02         7.46        40.77        24.03 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2348 
       21.14         1.74        22.32        29.00        25.02       180.20 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1722 
      116.12         9.40         2.14         5.42        20.52         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        18.54        27.88        31.79        28.47 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 
        5.79        11.41        13.02        34.13        31.30        48.92 
TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2002 
       56.61        43.43        15.75        38.17         5.52        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
        4.01        30.64        30.64        45.40         4.80         4.77 
TCGA-61-2094 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 
       71.74        60.62        55.50         6.48        76.87        20.68 
TCGA-61-2111 TCGA-61-2113 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
      125.75        22.22        18.94         0.79         8.05 

$`DEL PEAK 11(5Q13.2) WILD-TYPE`
TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1362 TCGA-04-1364 
        2.01        11.87        65.52        48.76        44.32        33.67 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 TCGA-04-1652 
       82.39        56.55        38.37       119.08        55.43        31.86 
TCGA-04-1655 TCGA-09-1659 TCGA-09-1664 TCGA-09-1666 TCGA-09-1672 TCGA-09-1673 
       45.37         9.99        74.93        57.60         5.85         3.02 
TCGA-09-2048 TCGA-09-2051 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0930 
        4.54        63.09        39.75        12.46        25.91        33.24 
TCGA-10-0936 TCGA-13-0714 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0758 
       35.80         6.21        31.10        15.19         2.50        11.38 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0807 TCGA-13-0883 TCGA-13-0910 TCGA-13-0912 
        8.45        38.93        13.61        68.94        37.08        34.06 
TCGA-13-1477 TCGA-13-1485 TCGA-13-1487 TCGA-13-1494 TCGA-13-1495 TCGA-13-1498 
       54.64        20.68        22.39        38.20        49.25        37.61 
TCGA-13-1500 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-A5FU TCGA-20-0987 
       13.97         4.41         4.77         3.91         8.42        23.05 
TCGA-20-0996 TCGA-20-1683 TCGA-23-1030 TCGA-23-1111 TCGA-23-1120 TCGA-23-1121 
       72.20        25.38        29.13         3.22         4.27         6.38 
TCGA-23-1809 TCGA-23-2079 TCGA-24-0966 TCGA-24-0968 TCGA-24-1105 TCGA-24-1413 
        0.53        91.66         7.63        19.66        47.41         6.31 
TCGA-24-1416 TCGA-24-1426 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 TCGA-24-1474 
        6.38         5.36       105.99         9.11         1.18        22.22 
TCGA-24-1544 TCGA-24-1545 TCGA-24-1551 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 
       26.96        57.40        51.91        88.50        44.09        45.50 
TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1844 TCGA-24-2036 TCGA-24-2038 
       47.70        10.26        90.15         3.72        64.01        44.52 
TCGA-24-2262 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 
        0.36        51.06        37.02        65.00         2.96        18.58 
TCGA-25-1628 TCGA-25-1632 TCGA-25-2042 TCGA-25-2393 TCGA-25-2399 TCGA-25-2408 
       20.61        56.94        13.02        38.04        19.99        31.00 
TCGA-29-1690 TCGA-29-1693 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1771 
       44.71       101.79        68.32         0.53        59.67        22.55 
TCGA-29-1774 TCGA-29-1785 TCGA-29-2429 TCGA-29-2436 TCGA-30-1714 TCGA-30-1853 
       17.33        34.62         4.90         9.76        38.07        36.26 
TCGA-30-1856 TCGA-30-1860 TCGA-30-1862 TCGA-30-1880 TCGA-30-1892 TCGA-31-1944 
       15.68        44.91         6.12        57.57        48.79        45.57 
TCGA-31-1950 TCGA-31-1951 TCGA-36-1568 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       18.77        22.49        28.77        21.53        22.85        22.55 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 TCGA-36-2537 
       25.74        27.85        24.23        35.05        29.49        25.91 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2548 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 
       23.80         2.24        14.17        16.18        26.04         9.44 
TCGA-42-2593 TCGA-57-1583 TCGA-57-1993 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 
        1.48        11.38        25.08        80.12        22.32        34.39 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1730 TCGA-61-1736 TCGA-61-1738 TCGA-61-1904 
       44.81        11.11         4.34        48.79        35.80         9.07 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 TCGA-61-1995 TCGA-61-2000 TCGA-61-2009 
       37.05        42.51        67.76         2.01        14.50        39.85 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
        1.18        45.96        51.72        61.64        58.39        65.52 
TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       44.52         6.35        31.07         8.61        39.68 

  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 
                        28.18                         27.85 
[1] "0.3 - 180.2 (28.2)" "0.4 - 119.1 (27.9)"
[1] "hr=" "1.2"
D44V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 11(5Q13.2) MUTATED         2   402                1
  DEL PEAK 11(5Q13.2) WILD-TYPE       0   155                1
D44V3, multiclass
                  clus
vv                 DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    402                           155
  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, continuous
D44V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q13.2) MUTATED     1 412
  DEL PEAK 11(5Q13.2) WILD-TYPE   2 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q13.2) MUTATED      1  412
  DEL PEAK 11(5Q13.2) WILD-TYPE    2  156
     clus
vv    DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE
  NO                            1                             2
  YES                         412                           156
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(5Q13.2) MUTATED    9 15  1  3
  DEL PEAK 11(5Q13.2) WILD-TYPE  5 11  4  0
D44V6, multiclass
    clus
vv   DEL PEAK 11(5Q13.2) MUTATED DEL PEAK 11(5Q13.2) WILD-TYPE
  R0                           9                             5
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(5Q13.2) MUTATED                                  1    14
  DEL PEAK 11(5Q13.2) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(5Q13.2) MUTATED                          20
  DEL PEAK 11(5Q13.2) WILD-TYPE                        12
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(5Q13.2) MUTATED                                           1   348
  DEL PEAK 11(5Q13.2) WILD-TYPE                                         0   127
D44V7, multiclass
                                           clus
vv                                          DEL PEAK 11(5Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             348
                                           clus
vv                                          DEL PEAK 11(5Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                 4
  BLACK OR AFRICAN AMERICAN                                            12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               127
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q13.2) MUTATED     7 237
  DEL PEAK 11(5Q13.2) WILD-TYPE   3  88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q13.2) MUTATED      7  237
  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                         237
                        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   173 187
  DEL PEAK 12(6Q27) WILD-TYPE  93 103
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        360                         196 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                        187                         103 
$`DEL PEAK 12(6Q27) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1347 
       40.24        41.00         1.81         2.01        46.62        63.09 
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-04-1514 TCGA-04-1517 TCGA-04-1530 TCGA-04-1536 
       76.57        71.47        56.55        19.99       119.08        29.10 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
       84.20        55.43        27.88        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 
       45.37        29.16         9.47        17.98         9.99        38.43 
TCGA-09-1662 TCGA-09-1665 TCGA-09-1666 TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 
       89.33        41.62        57.60        55.36        17.98         5.85 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
       97.55         6.12        35.15       112.41        63.09        39.75 
TCGA-09-2055 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       26.93        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       33.24        32.28        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 
        6.21        24.59        44.55        12.39        31.10        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        34.06        32.25 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 TCGA-13-0793 TCGA-13-0797 TCGA-13-0799 
       31.04        21.40        36.72        28.70         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 
        8.12         8.28         8.19        43.86        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0905 TCGA-13-0906 
       69.01        57.47        56.15        57.07        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        27.72        29.98        21.17        14.89 
TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        4.64         6.41         6.08         6.61         7.36         6.05 
TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 
        6.84         4.70         4.21         5.33        87.06        61.71 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 
       29.42        98.04        70.82        82.88        52.44        38.20 
TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       49.25        54.31        38.40        13.97        32.84         4.21 
TCGA-13-1506 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2061 
        4.41         4.18         2.56         3.91         3.09        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-1685 TCGA-20-1686 
        8.75         6.28        54.77        23.05        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.66        47.54        42.54        15.39        26.83        31.76 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        8.81        29.13        18.90         2.24        51.35        54.51 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 
       31.20        33.30        86.01       129.96         4.27        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         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-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
       11.64        21.80         7.66        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 
        6.31         6.38         7.82         0.76         6.25         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 
        5.95         5.36         4.83        17.39        28.37        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 
       43.53         8.55        72.92        45.14       105.99         1.18 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1556 
       57.40        64.27        41.06        51.91        41.39        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-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 
       17.23        90.15        88.37        38.24         8.32         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1849 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 
        3.81         4.37         5.79        22.68        16.44         4.87 
TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2029 TCGA-24-2036 TCGA-24-2261 
      152.02        44.84        58.16        14.43        64.01         0.79 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
       47.54        31.63        70.45        67.36        16.64        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1313 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
       55.86        53.26        26.96        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        36.95        33.96         2.99        12.00         2.96 
TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 
       20.61         7.86        56.94        85.05        13.02        49.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 
        1.02         3.02        45.01        19.99         2.96        29.03 
TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       26.99        78.90       101.79        38.53        33.70        31.20 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       18.25        41.98        85.68        66.81        62.93        39.12 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 
       31.23        22.98        24.36        22.55        12.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2425 TCGA-29-2427 
       12.30         8.38         5.36        34.62        65.00        62.47 
TCGA-29-2428 TCGA-29-2432 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 
       45.11        11.84        11.47        38.07        51.91        36.26 
TCGA-30-1855 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1866 
        2.47         0.26        48.10        44.91        34.78        36.62 
TCGA-30-1880 TCGA-30-1892 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       57.57        48.79        30.18        22.49         6.71        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-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       30.08        24.23        33.01        29.49        25.91        25.08 
TCGA-36-2542 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2552 
       21.60        20.98        18.31        20.52        14.17        11.47 
TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-57-1582 
       26.04         9.44        42.02         7.46        40.77        24.03 
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-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        2.14        44.81        20.52        20.94        31.43        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-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
        2.43         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-61-1918 
        9.07        34.13        37.05        48.92        56.61        15.75 
TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         2.01         5.52        17.98         4.01        30.64 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2104 
       30.64         4.80        58.39        60.62        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
       20.68        44.52         6.35        31.07         8.61        39.68 

$`DEL PEAK 12(6Q27) WILD-TYPE`
TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1356 TCGA-04-1364 
       49.15        18.51        11.87        65.52        49.28        33.67 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 
       82.39        41.59        38.37        48.89        28.64        64.64 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1664 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 
       57.76        35.57        74.93        61.87        30.51         3.02 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2050 TCGA-09-2054 TCGA-10-0933 
        8.55         6.18         4.54        71.11        20.94        11.70 
TCGA-10-0934 TCGA-13-0723 TCGA-13-0724 TCGA-13-0727 TCGA-13-0730 TCGA-13-0768 
        3.91        39.58         2.73        15.19        17.82         8.45 
TCGA-13-0791 TCGA-13-0794 TCGA-13-0795 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
       38.93        30.35        19.59        35.28        35.28        13.61 
TCGA-13-0893 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0912 TCGA-13-0920 
       43.36        19.36        47.38        48.33        34.06        13.81 
TCGA-13-1403 TCGA-13-1408 TCGA-13-1477 TCGA-13-1485 TCGA-13-1487 TCGA-13-1492 
       10.88         5.92        54.64        20.68        22.39        73.55 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1504 TCGA-13-1507 TCGA-13-2057 TCGA-13-2059 
        4.24        37.61        16.57         4.77        14.24        12.23 
TCGA-13-2060 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 
        8.61         8.42        25.94        26.20        72.20        27.52 
TCGA-20-1683 TCGA-20-1684 TCGA-23-1023 TCGA-23-1028 TCGA-23-1111 TCGA-23-1114 
       25.38        19.10        40.54        49.41         3.22        68.68 
TCGA-23-1116 TCGA-23-1121 TCGA-23-2077 TCGA-24-0968 TCGA-24-0979 TCGA-24-1104 
        4.57         6.38       115.89        19.66        41.56        63.55 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1431 TCGA-24-1464 TCGA-24-1469 TCGA-24-1470 
        7.99         7.86        19.17        12.46         9.11         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1553 TCGA-24-1555 
       22.22        26.96        16.21        56.58        58.09        88.50 
TCGA-24-1565 TCGA-24-1614 TCGA-24-1843 TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 
       10.26        48.33         3.48        11.28         5.52         9.80 
TCGA-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2026 TCGA-24-2027 TCGA-24-2030 
       30.21        11.05        81.11        34.82       109.71        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2254 TCGA-24-2260 TCGA-24-2262 
       18.48        28.18        44.52        57.07        36.16         0.36 
TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-25-1312 TCGA-25-1314 TCGA-25-1319 
       44.61         0.82        36.23         1.02        32.02        65.00 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1631 TCGA-25-1633 
       18.58        18.02        15.81         0.36         0.30        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2393 
       35.54        51.22        14.96        24.99        18.05        38.04 
TCGA-25-2397 TCGA-25-2400 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 
       12.00        42.02        31.00        44.71        47.18         0.79 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 
       68.32         0.53        16.90        18.67        59.67        29.23 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 TCGA-29-2414 
       34.62        17.00        17.33        14.93         7.23        86.17 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1862 
        4.90        42.25         9.76        21.04        15.68         6.12 
TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 TCGA-31-1944 TCGA-31-1950 TCGA-31-1959 
        1.22        24.26        30.05        45.57        18.77         2.20 
TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 
        8.55        25.74        27.85        24.69        35.05        29.82 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2587 
       23.80         2.24         6.05        16.18         7.99        23.74 
TCGA-42-2593 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 
        1.48        22.32        29.00        25.08        25.02        80.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 TCGA-61-1738 
        9.40        34.39         5.42        11.11         8.09        35.80 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 
       33.67        43.69        31.30        42.51        67.76        43.43 
TCGA-61-2000 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2088 
       14.50        39.85         1.18        45.96        45.40         4.77 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2102 TCGA-61-2111 
       51.72        71.74        61.64        65.52         6.48       125.75 
TCGA-61-2113 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       22.22        18.94         0.79         8.05 

  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                      125.75 
  DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE 
                     29.455                      24.840 
[1] "0.3 - 180.2 (29.5)" "0.3 - 125.8 (24.8)"
[1] "hr=" "1.2"
D45V2, continuous
                             vv
clus                          OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 12(6Q27) MUTATED         1   362                1
  DEL PEAK 12(6Q27) WILD-TYPE       1   195                1
D45V3, multiclass
                  clus
vv                 DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  OMENTUM                                  1                           1
  OVARY                                  362                         195
  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, continuous
D45V5, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED     2 371
  DEL PEAK 12(6Q27) WILD-TYPE   1 197
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED      2  371
  DEL PEAK 12(6Q27) WILD-TYPE    1  197
     clus
vv    DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  NO                          2                           1
  YES                       371                         197
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK 12(6Q27) MUTATED    8 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                         8                           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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q27) MUTATED                                  2    13
  DEL PEAK 12(6Q27) WILD-TYPE                                1     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(6Q27) MUTATED                          19
  DEL PEAK 12(6Q27) WILD-TYPE                        13
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(6Q27) MUTATED                                           1   307
  DEL PEAK 12(6Q27) WILD-TYPE                                         0   168
D45V7, multiclass
                                           clus
vv                                          DEL PEAK 12(6Q27) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                            13
  BLACK OR AFRICAN AMERICAN                                        19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         1
  WHITE                                                           307
                                           clus
vv                                          DEL PEAK 12(6Q27) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             168
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                             cls
clus                            0   1
  DEL PEAK 12(6Q27) MUTATED     7 214
  DEL PEAK 12(6Q27) WILD-TYPE   3 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 12(6Q27) MUTATED      7  214
  DEL PEAK 12(6Q27) WILD-TYPE    3  111
                        clus
vv                       DEL PEAK 12(6Q27) MUTATED DEL PEAK 12(6Q27) WILD-TYPE
  HISPANIC OR LATINO                             7                           3
  NOT HISPANIC OR LATINO                       214                         111
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 13(7P22.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7P22.1) MUTATED   119 124
  DEL PEAK 13(7P22.1) WILD-TYPE 147 166
  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                          243                           313 
  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                          124                           166 
$`DEL PEAK 13(7P22.1) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
       40.24        49.15        46.62        63.09        21.57        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 
       49.28        32.52        44.32        82.39        56.55        19.99 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1651 TCGA-09-1659 TCGA-09-1665 
       38.37       119.08        29.10        36.23         9.99        41.62 
TCGA-09-1666 TCGA-09-1668 TCGA-09-1673 TCGA-09-2044 TCGA-09-2045 TCGA-09-2050 
       57.60        55.36         3.02         6.12        35.15        71.11 
TCGA-09-2053 TCGA-09-2055 TCGA-10-0928 TCGA-10-0931 TCGA-10-0935 TCGA-10-0937 
       39.75        26.93        18.51        32.28        35.44        15.12 
TCGA-10-0938 TCGA-13-0724 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 
       19.86         2.73        55.17         2.50        11.38        11.54 
TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
        8.71         8.12         8.28        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       66.67        67.99        69.01        43.36        57.47        57.07 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
       47.38        48.33        44.94        34.06        29.98        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1409 TCGA-13-1412 TCGA-13-1481 TCGA-13-1487 
        6.08        10.88         6.84         5.33        87.06        22.39 
TCGA-13-1488 TCGA-13-1497 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 
       70.82        54.31        38.40        13.97        32.84         4.21 
TCGA-13-1509 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 TCGA-13-A5FT TCGA-20-1684 
        4.18         8.61        10.78         6.28        54.77        19.10 
TCGA-20-1685 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 TCGA-23-1026 TCGA-23-1027 
       16.70        47.54        42.54        40.54        26.83        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1110 TCGA-23-1114 
       49.41         8.81        18.90        51.35        54.51        68.68 
TCGA-23-1117 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 TCGA-23-2078 TCGA-23-2079 
       33.30       129.96         6.38        39.09        87.48        91.66 
TCGA-23-2084 TCGA-23-2641 TCGA-23-2645 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
       49.84         2.76         4.50        41.56        22.32        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 
       63.55        47.41         5.95         4.83        18.67        43.53 
TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 
        8.55        72.92        12.46        57.40        64.27        16.21 
TCGA-24-1550 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1562 TCGA-24-1563 
       41.06        41.39        70.62        39.88        45.50        47.70 
TCGA-24-1567 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       17.23         8.32         3.48         3.72         4.37        11.28 
TCGA-24-1849 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 
        5.79         5.52         9.80        30.21        16.44        81.11 
TCGA-24-2019 TCGA-24-2027 TCGA-24-2030 TCGA-24-2254 TCGA-24-2262 TCGA-24-2267 
        4.87       109.71        53.95        57.07         0.36        47.54 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2298 TCGA-25-1315 TCGA-25-1317 TCGA-25-1318 
       70.45         0.82        53.26        51.06         1.02        34.98 
TCGA-25-1321 TCGA-25-1322 TCGA-25-1630 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 
       33.96         2.99         7.86        56.94        60.59        51.22 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 
       13.02        49.05         1.02         3.02        19.99        42.02 
TCGA-25-2401 TCGA-25-2404 TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1697 
        2.96        29.03        78.90        47.18       101.79        31.20 
TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 
       16.90        18.67        59.67        18.25        34.62        17.00 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 
       85.68        62.93        39.12        22.98        24.36        11.84 
TCGA-29-1777 TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 
       12.30         8.38         5.36        86.17        65.00        62.47 
TCGA-29-2428 TCGA-29-2431 TCGA-30-1718 TCGA-30-1853 TCGA-30-1860 TCGA-30-1866 
       45.11        42.25        51.91        36.26        44.91        36.62 
TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1944 TCGA-31-1950 TCGA-31-1953 
       24.26        30.05        48.79        45.57        18.77         6.71 
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-42-2589 TCGA-42-2591 TCGA-57-1582 TCGA-57-1583 
       11.47        26.04        42.02        40.77        24.03        11.38 
TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 
        1.74        29.00        25.08        25.02       116.12         9.40 
TCGA-59-2354 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 
       34.39         5.42        20.52         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-61-2096 TCGA-61-2102 TCGA-61-2109 TCGA-61-2111 TCGA-61-2612 
        4.80        58.39         6.48        20.68       125.75         6.35 
TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
       39.68         0.79         8.05 

$`DEL PEAK 13(7P22.1) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       41.00         1.81         2.01        18.51        11.87        65.52 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1516 
       48.76        63.98        33.67        76.57        71.47        41.59 
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-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1667 
       17.98        35.57        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-10-0925 
        4.54       112.41        63.09        20.94        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 
       25.91        81.47        33.24        11.70         3.91        35.80 
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        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       15.19        17.82        11.18        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
       19.59         7.79         8.19        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0899 TCGA-13-0901 
       13.61        74.27        70.39        61.84        56.15        19.36 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0916 TCGA-13-0919 
       47.84        44.84        37.08        27.72        21.17        14.89 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        4.64         6.41         6.61         7.36         6.05         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.70         4.21        54.64        61.71        29.42        98.04 
TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       20.68        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1510 
        4.24        37.61        16.57         4.41         4.77         2.56 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 TCGA-13-A5FU 
        3.91         3.09        14.24        12.23         8.75         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1682 TCGA-20-1683 
       23.05        25.94        26.20        72.20        27.52        25.38 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1111 
        2.93         2.66        15.39        29.13         2.24         3.22 
TCGA-23-1113 TCGA-23-1116 TCGA-23-1118 TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 
       31.20         4.57        86.01         4.27        33.47        58.13 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2643 TCGA-24-0966 
        0.53        24.95       115.89        77.00         4.70         7.63 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1413 TCGA-24-1416 
       19.66        11.64        21.80         7.66         6.31         6.38 
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-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1466 TCGA-24-1467 
        5.36        17.39        28.37        19.17        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1549 
        9.11         3.45         1.18        22.22        26.96        56.58 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 
       51.91        58.09        88.50        19.53        44.09        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1845 
       10.26        90.15        88.37        48.33        38.24         3.81 
TCGA-24-1923 TCGA-24-1928 TCGA-24-2020 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 
       22.68        11.05       152.02        44.84        58.16        34.82 
TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       14.43        18.48        28.18        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 
        0.79        31.63        44.61        67.36        36.23        16.64 
TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1316 
       33.11        55.86         1.02        26.96        32.02        37.02 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       65.00        36.95        12.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 
       15.81         0.36        20.61         0.30        35.54        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2393 TCGA-25-2397 TCGA-25-2398 
       24.99        18.05        85.05        38.04        12.00        45.01 
TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       31.00        26.99        44.71        38.53         0.79        33.70 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 TCGA-29-1768 
       68.32         0.53        41.98        29.23        66.81        31.23 
TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 TCGA-29-1783 TCGA-29-1785 
       22.55        17.33        12.36        14.93         7.23        34.62 
TCGA-29-2429 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 
        4.90        11.84        11.47         9.76        21.04        38.07 
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-30-1867 TCGA-30-1880 TCGA-31-1946 TCGA-31-1951 TCGA-31-1956 TCGA-31-1959 
        1.22        57.57        30.18        22.49        44.12         2.20 
TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 
        8.55        30.08        25.74        24.23        24.69        35.05 
TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       29.49        25.91        25.08        23.80        21.60         2.24 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2587 TCGA-42-2588 
       14.17         6.05        16.18         7.99        23.74         9.44 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1584 TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 
        7.46         1.48        21.14        22.32       180.20        80.12 
TCGA-59-2350 TCGA-59-2355 TCGA-59-2372 TCGA-61-1721 TCGA-61-1727 TCGA-61-1730 
       22.32         2.14        44.81        11.11        18.54         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1900 
       31.79        28.47        33.67        43.69         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1907 TCGA-61-1911 TCGA-61-1918 
       11.41        13.02         9.07        31.30        42.51        15.75 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
        5.52        14.50         4.01         1.18        45.96        45.40 
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-61-2113 TCGA-61-2613 TCGA-61-2614 
       55.50        76.87        44.52        22.22        31.07         8.61 
TCGA-OY-A56Q 
       18.94 

  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                         0.36                          0.26 
  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                       129.96                        180.20 
  DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE 
                        32.28                         24.99 
[1] "0.4 - 130.0 (32.3)" "0.3 - 180.2 (25.0)"
[1] "hr=" "1.2"
D46V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 13(7P22.1) MUTATED         0   245                1
  DEL PEAK 13(7P22.1) WILD-TYPE       2   312                1
D46V3, multiclass
                  clus
vv                 DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE
  OMENTUM                                    0                             2
  OVARY                                    245                           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, continuous
D46V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(7P22.1) MUTATED     1 249
  DEL PEAK 13(7P22.1) WILD-TYPE   2 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.1) MUTATED      1  249
  DEL PEAK 13(7P22.1) WILD-TYPE    2  319
     clus
vv    DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE
  NO                            1                             2
  YES                         249                           319
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 13(7P22.1) MUTATED    8  8  2  1
  DEL PEAK 13(7P22.1) WILD-TYPE  6 18  3  2
D46V6, multiclass
    clus
vv   DEL PEAK 13(7P22.1) MUTATED DEL PEAK 13(7P22.1) WILD-TYPE
  R0                           8                             6
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(7P22.1) MUTATED                                  2    10
  DEL PEAK 13(7P22.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(7P22.1) MUTATED                          15
  DEL PEAK 13(7P22.1) WILD-TYPE                        17
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(7P22.1) MUTATED                                           0   206
  DEL PEAK 13(7P22.1) WILD-TYPE                                         1   269
D46V7, multiclass
                                           clus
vv                                          DEL PEAK 13(7P22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              10
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                             206
                                           clus
vv                                          DEL PEAK 13(7P22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                            17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               269
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(7P22.1) MUTATED     5 139
  DEL PEAK 13(7P22.1) WILD-TYPE   5 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7P22.1) MUTATED      5  139
  DEL PEAK 13(7P22.1) WILD-TYPE    5  186
                        clus
vv                       DEL PEAK 13(7P22.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         139
                        clus
vv                       DEL PEAK 13(7P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           186
[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   187 186
  DEL PEAK 14(8P23.3) WILD-TYPE  79 104
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          373                           183 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                          186                           104 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 
       40.24        41.00        46.62        65.52        48.76        21.57 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 
       71.47        82.39        41.59        19.99        38.37       119.08 
TCGA-04-1646 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 
       27.88        31.86        47.70        45.37        57.76        17.98 
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-09-1673 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
       30.51        17.98         3.02        97.55         6.18         6.12 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 
       71.11        63.09        20.94        12.46        54.31        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0936 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       18.51        33.24        35.80        39.58         2.73        12.39 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 
       31.10        17.82         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 
       34.06        31.04        21.40         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       30.35        19.59         8.71         7.79         8.28         8.19 
TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       43.86        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0887 TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 
       66.67        67.99        43.36        57.47        56.15        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0911 
       19.36        47.38        47.84        44.94        44.84        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0924 
       34.06        29.98        21.17        14.89        13.81         6.08 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 
        6.61         6.05         5.92         4.70         4.21        87.06 
TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1494 
       61.71        29.42        98.04        22.39        82.88        38.20 
TCGA-13-1495 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       49.25        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
        4.21         4.77         4.18         2.56         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        8.61        10.78         8.75         6.28        54.77         8.42 
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-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 
        2.93        47.54        42.54        15.39        26.83        31.76 
TCGA-23-1028 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       49.41        18.90        68.68         4.57        86.01       129.96 
TCGA-23-1120 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 
        4.27        33.47        58.13         0.53        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-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50        19.66        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-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
        7.86         0.76         6.25         6.02         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1464 TCGA-24-1466 TCGA-24-1470 
       19.17        18.67         8.55        12.46        45.14         3.45 
TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
       22.22        26.96        64.27        16.21        56.58        41.06 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1563 
       41.39        58.09        88.50        70.62        19.53        47.70 
TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 
       17.23        88.37        48.33         8.32         3.48         3.72 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1850 TCGA-24-1920 TCGA-24-1924 TCGA-24-1927 
        3.81         4.37         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-24-2030 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 
      109.71        53.95        28.18        57.07        36.16         0.79 
TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 
       70.45         0.82        67.36        36.23        16.64        55.86 
TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 
        1.02        26.96        32.02        51.06        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 
       36.95        33.96         2.99        12.00        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 TCGA-25-1635 
       15.81         0.36         7.86         0.30        60.59        51.22 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       18.05        85.05        13.02         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
       12.00        19.99        42.02         2.96        29.03        26.99 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       47.18       101.79        38.53         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
        0.53        16.90        18.67        59.67        41.98        29.23 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1770 TCGA-29-1774 
       17.00        85.68        62.93        39.12        24.36        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       12.36        11.84        12.30         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         4.90        11.84        11.47 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 
       51.91         2.47        15.68        44.91        34.78         6.12 
TCGA-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1944 TCGA-31-1946 
       36.62         1.22        24.26        48.79        45.57        30.18 
TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-36-1569 TCGA-36-1570 
       18.77        22.49        42.51        44.12        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-36-2534 TCGA-36-2537 
       24.23        24.69        35.05        33.01        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-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 
        6.05        11.47         7.99        26.04        23.74        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1585 TCGA-57-1586 
        7.46         1.48        24.03        11.38         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08        25.02       180.20        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1722 
        9.40        34.39         2.14         5.42        20.52         8.09 
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-61-1900 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 
       33.67         1.45         5.79        13.02         9.07        34.13 
TCGA-61-1907 TCGA-61-1910 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1919 
       31.30        37.05        56.61        67.76        15.75        38.17 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 
        5.52        14.50        17.98        30.64         1.18        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2102 
        4.80         4.77        60.62        65.52        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 
       76.87        44.52       125.75        22.22        31.07         8.61 
TCGA-WR-A838 
        8.05 

$`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-04-1514 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       63.98        56.55        29.10        84.20        55.43        48.89 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 
       28.64        64.64        36.23        29.16         9.47        35.57 
TCGA-09-1659 TCGA-09-1664 TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 
        9.99        74.93         5.85         8.55        35.15         4.54 
TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 TCGA-10-0926 TCGA-10-0931 TCGA-10-0933 
      112.41        39.75        26.93        25.91        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        15.12        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0727 TCGA-13-0751 TCGA-13-0762 TCGA-13-0793 TCGA-13-0800 
       44.55        15.19        55.17        32.25        28.70         8.12 
TCGA-13-0804 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0904 
       35.28        74.27        70.39        61.84        69.01        48.33 
TCGA-13-0910 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1405 TCGA-13-1409 
       37.08         4.64         6.41        10.88         7.36         6.84 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 
        5.33        54.64        20.68        70.82        52.44        73.55 
TCGA-13-1496 TCGA-13-1497 TCGA-13-1506 TCGA-13-1511 TCGA-13-2057 TCGA-20-0987 
        4.24        54.31         4.41         3.91        14.24        23.05 
TCGA-20-0996 TCGA-20-1687 TCGA-23-1023 TCGA-23-1029 TCGA-23-1030 TCGA-23-1032 
       72.20         2.66        40.54         8.81        29.13         2.24 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1117 TCGA-23-1121 
       51.35        54.51         3.22        31.20        33.30         6.38 
TCGA-23-1122 TCGA-24-0966 TCGA-24-0970 TCGA-24-1418 TCGA-24-1425 TCGA-24-1426 
       39.09         7.63        11.64         7.99         5.95         5.36 
TCGA-24-1430 TCGA-24-1435 TCGA-24-1463 TCGA-24-1467 TCGA-24-1469 TCGA-24-1471 
       28.37        43.53        72.92       105.99         9.11         1.18 
TCGA-24-1545 TCGA-24-1551 TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 
       57.40        51.91        39.88        44.09        45.50        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1616 TCGA-24-1847 TCGA-24-1849 TCGA-24-1923 
       10.26        90.15        38.24        11.28         5.79        22.68 
TCGA-24-2026 TCGA-24-2029 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 
       34.82        14.43        18.48        64.01        44.52         0.36 
TCGA-24-2267 TCGA-24-2271 TCGA-24-2281 TCGA-24-2295 TCGA-24-2298 TCGA-25-1316 
       47.54        31.63        44.61        33.11        53.26        37.02 
TCGA-25-1317 TCGA-25-1329 TCGA-25-1628 TCGA-25-1632 TCGA-25-1634 TCGA-25-1870 
        1.02         2.96        20.61        56.94        35.54        14.96 
TCGA-25-1871 TCGA-25-2391 TCGA-25-2398 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       24.99        49.05        45.01        31.00        78.90        44.71 
TCGA-29-1696 TCGA-29-1705 TCGA-29-1711 TCGA-29-1763 TCGA-29-1768 TCGA-29-1769 
       33.70        18.25        34.62        66.81        31.23        22.98 
TCGA-29-1771 TCGA-29-1778 TCGA-29-1785 TCGA-29-2427 TCGA-29-2431 TCGA-29-2436 
       22.55        14.93        34.62        62.47        42.25         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1857 TCGA-30-1859 TCGA-30-1880 
       21.04        38.07        36.26         0.26        48.10        57.57 
TCGA-30-1891 TCGA-31-1953 TCGA-31-1959 TCGA-36-1568 TCGA-36-2532 TCGA-36-2540 
       30.05         6.71         2.20        28.77        29.49        23.80 
TCGA-36-2548 TCGA-36-2551 TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 TCGA-59-2349 
       14.17        16.18         9.44        40.77        21.14        80.12 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1724 TCGA-61-1725 TCGA-61-1734 TCGA-61-1736 
       44.81        11.11        20.94        31.43        28.47        48.79 
TCGA-61-1738 TCGA-61-1743 TCGA-61-1899 TCGA-61-1901 TCGA-61-1911 TCGA-61-1913 
       35.80        43.69         8.42        11.41        42.51        48.92 
TCGA-61-1917 TCGA-61-1995 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 
       43.43         2.01         4.01        30.64        39.85        45.96 
TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 TCGA-61-2109 TCGA-61-2612 
       51.72        71.74        61.64        58.39        20.68         6.35 
TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       39.68        18.94         0.79 

  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                        112.41 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                        25.94                         31.00 
[1] "0.3 - 180.2 (25.9)" "0.3 - 112.4 (31.0)"
[1] "hr=" "1.2"
D47V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 14(8P23.3) MUTATED         2   373                2
  DEL PEAK 14(8P23.3) WILD-TYPE       0   184                0
D47V3, multiclass
                  clus
vv                 DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    373                           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, continuous
D47V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     2 381
  DEL PEAK 14(8P23.3) WILD-TYPE   1 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      2  381
  DEL PEAK 14(8P23.3) WILD-TYPE    1  187
     clus
vv    DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  NO                            2                             1
  YES                         381                           187
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 14(8P23.3) MUTATED   10 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                          10                             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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(8P23.3) MUTATED                                  3    12
  DEL PEAK 14(8P23.3) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(8P23.3) MUTATED                          21
  DEL PEAK 14(8P23.3) WILD-TYPE                        11
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(8P23.3) MUTATED                                           1   315
  DEL PEAK 14(8P23.3) WILD-TYPE                                         0   160
D47V7, multiclass
                                           clus
vv                                          DEL PEAK 14(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              12
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             315
                                           clus
vv                                          DEL PEAK 14(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     9 216
  DEL PEAK 14(8P23.3) WILD-TYPE   1 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      9  216
  DEL PEAK 14(8P23.3) WILD-TYPE    1  109
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               9
  NOT HISPANIC OR LATINO                         216
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           109
[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   193 198
  DEL PEAK 15(8P21.2) WILD-TYPE  73  92
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          391                           165 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                          198                            92 
$`DEL PEAK 15(8P21.2) MUTATED`
TCGA-04-1332 TCGA-04-1338 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1351 
       41.00        46.62        65.52        48.76        21.57        65.46 
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        71.47 
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-04-1638 TCGA-04-1646 TCGA-04-1652 TCGA-04-1655 TCGA-09-0366 TCGA-09-0367 
       55.43        27.88        31.86        45.37        57.76        17.98 
TCGA-09-1661 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 
       38.43        74.93        41.62        57.60        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 
       30.51        17.98         3.02         8.55         6.18         6.12 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0927 
       71.11        63.09        20.94        12.46        54.31        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 TCGA-13-0714 TCGA-13-0723 
       18.51        33.24        32.28        35.80         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        31.10        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        34.06        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.28         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 
       35.28        13.61        68.94        91.40        74.27        70.39 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0908 
       67.99        43.36        57.47        56.15        19.36        44.84 
TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 
       27.72        34.06        29.98        21.17        14.89        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 
        6.08        10.88         6.61         6.05         5.92         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
        4.21        87.06        61.71        29.42        98.04        22.39 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 
       82.88        52.44        38.20        49.25         4.24        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 
       38.40        13.97        32.84        16.57         4.21         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 
        4.18         2.56         3.09        12.23         8.61        10.78 
TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 
        8.75         6.28        54.77         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-23-1021 TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        42.54        15.39        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1031 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
        8.81        18.90        68.68         4.57        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 
        4.27         6.38        33.47        58.13         0.53        24.95 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
      115.89        87.48        91.66        49.84         2.76         4.70 
TCGA-23-2645 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.50        19.66        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-24-1419 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 
        7.86         0.76         6.25         6.02         4.83        17.39 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1464 TCGA-24-1467 
       19.17        18.67        43.53         8.55        12.46       105.99 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 
        3.45        22.22        26.96        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-24-1563 TCGA-24-1564 TCGA-24-1567 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 
       47.70        25.87        17.23        88.37        48.33         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-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2019 
        9.80        30.21        16.44        11.05        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        53.95 
TCGA-24-2033 TCGA-24-2035 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 
       18.48        28.18        57.07        36.16         0.79        47.54 
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-25-1312 TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 
       33.11        55.86         1.02        26.96        32.02        51.06 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 
       18.58        18.02        15.81         0.36         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 TCGA-25-1878 TCGA-25-2392 
       56.94        60.59        51.22        24.99        85.05         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-29-1691 TCGA-29-1694 TCGA-29-1695 TCGA-29-1697 
       29.03        26.99        47.18        38.53         0.79        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 
       68.32         0.53        16.90        18.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 
       29.23        34.62        17.00        85.68        62.93        39.12 
TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       31.23        24.36        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
       14.93         7.23         5.36        65.00        45.11         4.90 
TCGA-29-2432 TCGA-29-2434 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 
       11.84        11.47        51.91         2.47        15.68         0.26 
TCGA-30-1860 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-30-1891 
       44.91        34.78         6.12        36.62        24.26        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 
       45.57        30.18        18.77        22.49        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-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 
       35.05        29.82        25.91        25.08        21.60         2.24 
TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 
       20.98        18.31        20.52        11.47         7.99        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         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-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        20.52         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 
       27.88         4.34        31.79        44.84         2.43        33.67 
TCGA-61-1895 TCGA-61-1904 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 
        1.45         9.07        31.30        48.92        56.61        67.76 
TCGA-61-1918 TCGA-61-1919 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 
       15.75        38.17         5.52        14.50         4.01        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2096 TCGA-61-2097 
       30.64         1.18        45.40         4.80        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-VG-A8LO 
      125.75        22.22         6.35        31.07         8.61         0.79 
TCGA-WR-A838 
        8.05 

$`DEL PEAK 15(8P21.2) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       40.24         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1347 TCGA-04-1350 TCGA-04-1525 TCGA-04-1542 TCGA-04-1644 TCGA-04-1648 
       63.09        63.98        38.37        84.20        48.89        28.64 
TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 
       64.64        36.23        47.70        29.16         9.47        35.57 
TCGA-09-1659 TCGA-09-1662 TCGA-09-1672 TCGA-09-1675 TCGA-09-2045 TCGA-09-2048 
        9.99        89.33         5.85        97.55        35.15         4.54 
TCGA-09-2049 TCGA-09-2053 TCGA-09-2055 TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 
      112.41        39.75        26.93        25.91        11.70         3.91 
TCGA-10-0935 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0727 
       35.44        15.12        19.86        24.59        44.55        15.19 
TCGA-13-0751 TCGA-13-0800 TCGA-13-0884 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       55.17         8.12       107.18        66.67        61.84        69.01 
TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       57.07        47.38        48.33        47.84        44.94        37.08 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 TCGA-13-1409 TCGA-13-1412 TCGA-13-1477 
        4.64         6.41         7.36         6.84         5.33        54.64 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1492 TCGA-13-1497 TCGA-13-1506 TCGA-13-1511 
       20.68        70.82        73.55        54.31         4.41         3.91 
TCGA-13-2057 TCGA-20-0996 TCGA-20-1687 TCGA-23-1023 TCGA-23-1030 TCGA-23-1032 
       14.24        72.20         2.66        40.54        29.13         2.24 
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        37.02         1.02         2.96 
TCGA-25-1628 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       20.61        35.54        14.96        18.05        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        44.71       101.79        33.70 
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        34.62 
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        21.04        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 
       26.04        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 
       61.64        39.68        18.94 

  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                        112.41 
  DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE 
                        25.38                         34.82 
[1] "0.3 - 180.2 (25.4)" "0.4 - 112.4 (34.8)"
[1] "hr=" "1.1"
D48V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 15(8P21.2) MUTATED         2   390                2
  DEL PEAK 15(8P21.2) WILD-TYPE       0   167                0
D48V3, multiclass
                  clus
vv                 DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE
  OMENTUM                                    2                             0
  OVARY                                    390                           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, continuous
D48V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.2) MUTATED     2 398
  DEL PEAK 15(8P21.2) WILD-TYPE   1 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.2) MUTATED      2  398
  DEL PEAK 15(8P21.2) WILD-TYPE    1  170
     clus
vv    DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE
  NO                            2                             1
  YES                         398                           170
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 15(8P21.2) MUTATED    8 19  4  2
  DEL PEAK 15(8P21.2) WILD-TYPE  6  7  1  1
D48V6, multiclass
    clus
vv   DEL PEAK 15(8P21.2) MUTATED DEL PEAK 15(8P21.2) WILD-TYPE
  R0                           8                             6
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8P21.2) MUTATED                                  2    13
  DEL PEAK 15(8P21.2) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(8P21.2) MUTATED                          23
  DEL PEAK 15(8P21.2) WILD-TYPE                         9
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 15(8P21.2) MUTATED                                           1   332
  DEL PEAK 15(8P21.2) WILD-TYPE                                         0   143
D48V7, multiclass
                                           clus
vv                                          DEL PEAK 15(8P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              13
  BLACK OR AFRICAN AMERICAN                                          23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             332
                                           clus
vv                                          DEL PEAK 15(8P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                             9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               143
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P21.2) MUTATED     9 224
  DEL PEAK 15(8P21.2) WILD-TYPE   1 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P21.2) MUTATED      9  224
  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                         224
                        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   110 138
  DEL PEAK 16(9P24.3) WILD-TYPE 156 152
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          248                           308 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                          138                           152 
$`DEL PEAK 16(9P24.3) MUTATED`
TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 
        2.01        46.62        11.87        65.52        63.09        21.57 
TCGA-04-1350 TCGA-04-1351 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       63.98        65.46        32.52        44.32        33.67        76.57 
TCGA-04-1371 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       82.39        38.37        29.10        84.20        55.43        27.88 
TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 
       31.86        29.16         9.47        17.98        35.57         9.99 
TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 TCGA-09-1667 TCGA-09-1670 TCGA-09-1673 
       38.43        89.33        41.62        61.87        17.98         3.02 
TCGA-09-1675 TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2053 
       97.55         6.12         4.54       112.41        63.09        39.75 
TCGA-09-2054 TCGA-09-2056 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 
       20.94        12.46        81.47        18.51        33.24        32.28 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0724 TCGA-13-0730 
       15.12        19.86         6.21        24.59         2.73        17.82 
TCGA-13-0760 TCGA-13-0762 TCGA-13-0795 TCGA-13-0800 TCGA-13-0804 TCGA-13-0805 
       11.54        32.25        19.59         8.12        35.28        35.28 
TCGA-13-0883 TCGA-13-0885 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       68.94        91.40        74.27        70.39        61.84        67.99 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0906 TCGA-13-0908 TCGA-13-0921 
       56.15        57.07        19.36        44.94        44.84         4.64 
TCGA-13-0924 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
        6.08         6.84         4.70         4.21         5.33        87.06 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 
       29.42        20.68        82.88        52.44        38.20        49.25 
TCGA-13-1500 TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
       13.97         4.18         2.56        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0991 TCGA-20-1682 TCGA-23-1021 
        8.75        54.77         8.42        26.20        27.52        47.54 
TCGA-23-1022 TCGA-23-1027 TCGA-23-1030 TCGA-23-1031 TCGA-23-1114 TCGA-23-1118 
       42.54        31.76        29.13        18.90        68.68        86.01 
TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 
      129.96         6.38        33.47       115.89        87.48        77.00 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 
        4.70         4.50        11.64        22.32        47.41         6.31 
TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1426 TCGA-24-1427 TCGA-24-1430 
        7.99         7.86         0.76         5.36         4.83        28.37 
TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 TCGA-24-1545 TCGA-24-1550 TCGA-24-1552 
       19.17        72.92        12.46        57.40        41.06        41.39 
TCGA-24-1560 TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1843 
       44.09        25.87        17.23        90.15        88.37         3.48 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       44.84        58.16       109.71        14.43        53.95        28.18 
TCGA-24-2036 TCGA-24-2260 TCGA-24-2261 TCGA-24-2289 TCGA-24-2293 TCGA-24-2295 
       64.01        36.16         0.79        67.36        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        32.02        37.02         1.02 
TCGA-25-1318 TCGA-25-1321 TCGA-25-1323 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 
       34.98        33.96        12.00        18.02        15.81         0.36 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       56.94        60.59        35.54        14.96        24.99        18.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-29-1691 
        1.02        38.04        19.99        42.02         2.96        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1705 TCGA-29-1710 TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 
        0.53        18.25        29.23        39.12        24.36        22.55 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1783 TCGA-29-2425 TCGA-29-2429 TCGA-29-2431 
       17.33        12.36         7.23        65.00         4.90        42.25 
TCGA-29-2434 TCGA-29-2436 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
       11.47         9.76        38.07        51.91        36.26        15.68 
TCGA-30-1857 TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 TCGA-31-1955 TCGA-31-1959 
        0.26        34.78        36.62        30.05        42.51         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2534 
       29.10        22.85        30.08        24.23        35.05        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2542 TCGA-36-2548 TCGA-36-2549 
       25.91        25.08        23.80        21.60        14.17         6.05 
TCGA-36-2552 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       11.47        42.02         7.46         1.48        24.03        11.38 
TCGA-57-1992 TCGA-57-1994 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 
       29.00        25.02       116.12         9.40         5.42        44.81 
TCGA-59-A5PD TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1900 
       20.52        27.88         4.34        31.79        35.80         5.79 
TCGA-61-1903 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 TCGA-61-1914 TCGA-61-1915 
       13.02        31.30        37.05        42.51        56.61        67.76 
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-61-2095 
        4.01        30.64        39.85        30.64         1.18        61.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 TCGA-61-2113 
       60.62        65.52        55.50        76.87        20.68        22.22 
TCGA-61-2612 TCGA-VG-A8LO 
        6.35         0.79 

$`DEL PEAK 16(9P24.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1342 TCGA-04-1348 
       40.24        41.00         1.81        49.15        18.51        48.76 
TCGA-04-1356 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1530 
       49.28        71.47        56.55        41.59        19.99       119.08 
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-09-0366 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 TCGA-09-1669 TCGA-09-1672 
       57.76        74.93        57.60        55.36        30.51         5.85 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2045 TCGA-09-2050 TCGA-09-2055 TCGA-10-0925 
        8.55         6.18        35.15        71.11        26.93        54.31 
TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0720 
       25.91        11.70         3.91        35.44        35.80        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 
       39.58        12.39        31.10        15.19        55.17         2.50 
TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 
       11.18        11.38        34.06        31.04        21.40         8.45 
TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       38.93        36.72        28.70        30.35         8.71         7.79 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0807 TCGA-13-0884 TCGA-13-0887 
        8.28         8.19        43.86        13.61       107.18        66.67 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       69.01        43.36        57.47        47.38        48.33        47.84 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       37.08        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
       13.81         6.41        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1477 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
        5.92        54.64        61.71        98.04        22.39        70.82 
TCGA-13-1492 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       73.55         4.24        54.31        37.61        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-1512 
       16.57         4.21         4.41         4.77         3.91         3.09 
TCGA-13-2059 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
       12.23         6.28        23.05        25.94        72.20        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 TCGA-23-1024 
       19.10        16.70         2.93         2.66        40.54        15.39 
TCGA-23-1026 TCGA-23-1028 TCGA-23-1029 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
       26.83        49.41         8.81         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1120 TCGA-23-1122 
        3.22        31.20         4.57        33.30         4.27        39.09 
TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2079 TCGA-23-2084 TCGA-23-2641 
       58.13         0.53        24.95        91.66        49.84         2.76 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        7.63        19.66        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
       63.55         6.38         7.82         6.25         6.02         5.95 
TCGA-24-1428 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 
       17.39        18.67        43.53         8.55        45.14       105.99 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 
        9.11         3.45         1.18        22.22        26.96        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       16.21        56.58        51.91        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1614 
       39.88        19.53        45.50        47.70        10.26        48.33 
TCGA-24-1616 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 TCGA-24-1847 
       38.24         8.32         3.72         3.81         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-24-2026 TCGA-24-2033 
       11.05        81.11         4.87       152.02        34.82        18.48 
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-24-2288 TCGA-24-2290 TCGA-24-2297 TCGA-25-1315 TCGA-25-1319 
       44.61         0.82        36.23        55.86        51.06        65.00 
TCGA-25-1320 TCGA-25-1322 TCGA-25-1329 TCGA-25-1623 TCGA-25-1628 TCGA-25-1630 
       36.95         2.99         2.96        18.58        20.61         7.86 
TCGA-25-1631 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 
        0.30        51.22        85.05        13.02        49.05         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 
       12.00        45.01        29.03        31.00        26.99        78.90 
TCGA-29-1690 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1711 
       44.71        16.90        18.67        59.67        41.98        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 
       17.00        85.68        66.81        62.93        31.23        22.98 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 
       11.84        12.30        14.93         8.38         5.36        34.62 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2428 TCGA-29-2432 TCGA-29-A5NZ TCGA-30-1855 
       86.17        62.47        45.11        11.84        21.04         2.47 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 
       48.10        44.91         6.12         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-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       44.12        28.77        21.53        22.55         8.55        25.74 
TCGA-36-1578 TCGA-36-1581 TCGA-36-2530 TCGA-36-2532 TCGA-36-2543 TCGA-36-2544 
       27.85        24.69        33.01        29.49         2.24        20.98 
TCGA-36-2545 TCGA-36-2547 TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 
       18.31        20.52        16.18         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2591 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1993 
        9.44        40.77        21.14         1.74        22.32        25.08 
TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2354 TCGA-59-2355 TCGA-61-1721 
      180.20        80.12        22.32        34.39         2.14        11.11 
TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
        8.09        20.94        31.43        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 
       44.84         2.43        33.67        43.69         1.45         8.42 
TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1913 TCGA-61-1917 TCGA-61-2017 
       11.41         9.07        34.13        48.92        43.43        45.96 
TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2096 
       45.40         4.80         4.77        51.72        71.74        58.39 
TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P 
        6.48        44.52       125.75        31.07         8.61        39.68 
TCGA-OY-A56Q TCGA-WR-A838 
       18.94         8.05 

  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 
                       129.96                        180.20 
  DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE 
                       29.100                        26.945 
[1] "0.3 - 130.0 (29.1)" "0.3 - 180.2 (26.9)"
[1] "hr=" "1.1"
D49V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 16(9P24.3) MUTATED         1   248                2
  DEL PEAK 16(9P24.3) WILD-TYPE       1   309                0
D49V3, multiclass
                  clus
vv                 DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE
  OMENTUM                                    1                             1
  OVARY                                    248                           309
  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, continuous
D49V5, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P24.3) MUTATED     2 257
  DEL PEAK 16(9P24.3) WILD-TYPE   1 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P24.3) MUTATED      2  257
  DEL PEAK 16(9P24.3) WILD-TYPE    1  311
     clus
vv    DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE
  NO                            2                             1
  YES                         257                           311
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 16(9P24.3) MUTATED    8 11  3  1
  DEL PEAK 16(9P24.3) WILD-TYPE  6 15  2  2
D49V6, multiclass
    clus
vv   DEL PEAK 16(9P24.3) MUTATED DEL PEAK 16(9P24.3) WILD-TYPE
  R0                           8                             6
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(9P24.3) MUTATED                                  1     7
  DEL PEAK 16(9P24.3) WILD-TYPE                                2    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(9P24.3) MUTATED                          14
  DEL PEAK 16(9P24.3) WILD-TYPE                        18
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(9P24.3) MUTATED                                           1   211
  DEL PEAK 16(9P24.3) WILD-TYPE                                         0   264
D49V7, multiclass
                                           clus
vv                                          DEL PEAK 16(9P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               7
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             211
                                           clus
vv                                          DEL PEAK 16(9P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                11
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               264
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P24.3) MUTATED     4 147
  DEL PEAK 16(9P24.3) WILD-TYPE   6 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P24.3) MUTATED      4  147
  DEL PEAK 16(9P24.3) WILD-TYPE    6  178
                        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                           178
[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   160 168
  DEL PEAK 17(9Q34.13) WILD-TYPE 106 122
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           328                            228 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                           168                            122 
$`DEL PEAK 17(9Q34.13) MUTATED`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       41.00        49.15        46.62        11.87        65.52        63.09 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1364 TCGA-04-1371 TCGA-04-1516 
       48.76        21.57        63.98        33.67        82.39        41.59 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 
       19.99        38.37        29.10        84.20        55.43        27.88 
TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 
       28.64        64.64        36.23        31.86        45.37        29.16 
TCGA-09-0365 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
        9.47        17.98        35.57         9.99        38.43        89.33 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 
       61.87        30.51        17.98         3.02         8.55        97.55 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0927 TCGA-10-0930 TCGA-10-0935 
       20.94        26.93        54.31        81.47        33.24        35.44 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0730 TCGA-13-0751 
       19.86        24.59        44.55         2.73        17.82        55.17 
TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
        2.50        11.18        11.54        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 
        8.45        38.93        36.72        19.59         8.71         7.79 
TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.12         8.28        43.86        35.28        35.28        13.61 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0899 TCGA-13-0903 
      107.18        91.40        74.27        66.67        56.15        47.38 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0913 TCGA-13-0919 
       47.84        44.94        37.08        27.72        29.98        14.89 
TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1407 
       13.81         4.64         6.41         6.08        10.88         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1483 
        5.92         6.84         4.70         4.21        87.06        29.42 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 TCGA-13-1497 
       98.04        22.39        82.88        52.44        49.25        54.31 
TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       37.61        13.97        16.57         4.41         4.77         4.18 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.91        14.24        12.23         8.61        10.78         8.75 
TCGA-20-0990 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 
       25.94        27.52        25.38        19.10        16.70         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
        2.66        47.54        49.41         8.81        29.13        18.90 
TCGA-23-1110 TCGA-23-1111 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 
       54.51         3.22        68.68         4.57        86.01       129.96 
TCGA-23-1120 TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 
        4.27        58.13        24.95       115.89        77.00        49.84 
TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 
        4.70         4.50         7.63        19.66        21.80        41.56 
TCGA-24-0982 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1422 TCGA-24-1424 
       22.32        47.41         6.31         7.82         0.76         6.02 
TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1463 TCGA-24-1464 
        5.36        17.39        28.37        19.17        72.92        12.46 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        9.11         1.18        26.96        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       41.06        51.91        19.53        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 
       25.87        90.15        88.37        48.33        38.24         8.32 
TCGA-24-1843 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 TCGA-24-1924 TCGA-24-1928 
        3.48         3.81        11.28         5.79        30.21        11.05 
TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 
       81.11         4.87        44.84        58.16        34.82        14.43 
TCGA-24-2033 TCGA-24-2260 TCGA-24-2261 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 
       18.48        36.16         0.79        47.54        70.45         0.82 
TCGA-24-2293 TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 TCGA-25-1314 
       16.64        33.11        53.26         1.02        26.96        32.02 
TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 
       51.06        37.02         1.02        34.98        36.95        33.96 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1627 TCGA-25-1630 TCGA-25-1631 TCGA-25-1633 
        2.99        12.00         0.36         7.86         0.30        60.59 
TCGA-25-1634 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-2391 TCGA-25-2392 
       35.54        14.96        24.99        18.05        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-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1698 
        2.96        78.90        47.18       101.79         0.79        68.32 
TCGA-29-1699 TCGA-29-1702 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 
        0.53        18.67        29.23        34.62        85.68        66.81 
TCGA-29-1766 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.12        24.36        22.55        17.33        12.36        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2434 
        8.38         7.23         5.36        86.17        65.00        11.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 TCGA-30-1866 TCGA-30-1867 
       38.07        51.91        36.26         2.47        36.62         1.22 
TCGA-30-1880 TCGA-31-1944 TCGA-31-1946 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       57.57        45.57        30.18         6.71        42.51         2.20 
TCGA-36-1569 TCGA-36-1571 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       29.10        22.85        30.08        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 
       24.69        35.05         2.24        20.98        18.31        20.52 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       14.17         6.05        11.47         9.44        42.02         7.46 
TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 
       40.77         1.48        24.03        21.14         1.74        29.00 
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-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        27.88         4.34        31.79        28.47 
TCGA-61-1736 TCGA-61-1741 TCGA-61-1743 TCGA-61-1899 TCGA-61-1904 TCGA-61-1907 
       48.79        33.67        43.69         8.42         9.07        31.30 
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-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
        2.01        17.98         4.01        39.85        30.64         1.18 
TCGA-61-2018 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 
       45.40        71.74        58.39        60.62        65.52        55.50 
TCGA-61-2102 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
        6.48        44.52       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-WR-A838 
        8.61        39.68        18.94         8.05 

$`DEL PEAK 17(9Q34.13) WILD-TYPE`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1337 TCGA-04-1342 TCGA-04-1351 TCGA-04-1356 
       40.24         1.81         2.01        18.51        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1530 
       32.52        44.32        76.57        71.47        56.55       119.08 
TCGA-04-1644 TCGA-04-1654 TCGA-09-0366 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       48.89        47.70        57.76        74.93        41.62        57.60 
TCGA-09-1668 TCGA-09-1672 TCGA-09-2043 TCGA-09-2045 TCGA-09-2056 TCGA-10-0926 
       55.36         5.85         6.18        35.15        12.46        25.91 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 
       18.51        32.28        11.70         3.91        35.80        15.12 
TCGA-13-0714 TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0758 
        6.21        39.58        12.39        31.10        15.19        11.38 
TCGA-13-0761 TCGA-13-0793 TCGA-13-0794 TCGA-13-0802 TCGA-13-0883 TCGA-13-0888 
       34.06        28.70        30.35         8.19        68.94        70.39 
TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 
       61.84        67.99        69.01        43.36        57.47        57.07 
TCGA-13-0901 TCGA-13-0904 TCGA-13-0908 TCGA-13-0912 TCGA-13-0916 TCGA-13-1404 
       19.36        48.33        44.84        34.06        21.17         6.61 
TCGA-13-1405 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1488 
        7.36         5.33        54.64        61.71        20.68        70.82 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 
       73.55        38.20         4.24        38.40        32.84         4.21 
TCGA-13-1510 TCGA-13-1512 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
        2.56         3.09         6.28        54.77         8.42        23.05 
TCGA-20-0991 TCGA-20-0996 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       26.20        72.20        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1032 TCGA-23-1109 TCGA-23-1113 TCGA-23-1117 TCGA-23-1121 
       31.76         2.24        51.35        31.20        33.30         6.38 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2078 TCGA-23-2079 TCGA-23-2641 
       39.09        33.47         0.53        87.48        91.66         2.76 
TCGA-24-0970 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1418 
       11.64         7.66        54.12        63.55         6.38         7.99 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1425 TCGA-24-1427 TCGA-24-1434 TCGA-24-1435 
        7.86         6.25         5.95         4.83        18.67        43.53 
TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1474 TCGA-24-1546 
        8.55        45.14       105.99         3.45        22.22        64.27 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1565 
       41.39        58.09        88.50        70.62        39.88        10.26 
TCGA-24-1567 TCGA-24-1844 TCGA-24-1846 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 
       17.23         3.72         4.37         5.52         9.80        22.68 
TCGA-24-1927 TCGA-24-2020 TCGA-24-2027 TCGA-24-2030 TCGA-24-2035 TCGA-24-2036 
       16.44       152.02       109.71        53.95        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 
       44.52        57.07         0.36        31.63        44.61        67.36 
TCGA-24-2290 TCGA-24-2297 TCGA-25-1319 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 
       36.23        55.86        65.00         2.96        18.58        18.02 
TCGA-25-1626 TCGA-25-1628 TCGA-25-1632 TCGA-25-1635 TCGA-25-1878 TCGA-25-2042 
       15.81        20.61        56.94        51.22        85.05        13.02 
TCGA-25-2404 TCGA-25-2408 TCGA-25-2409 TCGA-29-1690 TCGA-29-1694 TCGA-29-1696 
       29.03        31.00        26.99        44.71        38.53        33.70 
TCGA-29-1697 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1761 
       31.20        16.90        59.67        18.25        41.98        17.00 
TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1776 TCGA-29-1778 TCGA-29-1785 
       62.93        31.23        22.98        11.84        14.93        34.62 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       62.47        45.11         4.90        42.25        11.84         9.76 
TCGA-29-A5NZ TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 
       21.04        15.68         0.26        48.10        44.91        34.78 
TCGA-30-1862 TCGA-30-1887 TCGA-30-1891 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 
        6.12        24.26        30.05        48.79        18.77        22.49 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-2530 
       44.12        28.77        21.53        22.55         8.55        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-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-57-1583 TCGA-57-1586 
       16.18         7.99        26.04        23.74        11.38        22.32 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-A5PD 
       25.08        25.02       180.20        80.12        22.32        20.52 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
       11.11         8.09        18.54        44.84        35.80         2.43 
TCGA-61-1895 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1910 
        1.45         5.79        11.41        13.02        34.13        37.05 
TCGA-61-1911 TCGA-61-1998 TCGA-61-2000 TCGA-61-2008 TCGA-61-2017 TCGA-61-2087 
       42.51         5.52        14.50        30.64        45.96         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2104 TCGA-61-2109 TCGA-VG-A8LO 
        4.77        51.72        61.64        76.87        20.68         0.79 

  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 
                        129.96                         180.20 
  DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE 
                        27.785                         28.900 
[1] "0.3 - 130.0 (27.8)" "0.3 - 180.2 (28.9)"
[1] "hr=" "1"  
D50V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 17(9Q34.13) MUTATED         1   330                2
  DEL PEAK 17(9Q34.13) WILD-TYPE       1   227                0
D50V3, multiclass
                  clus
vv                 DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     330                            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, continuous
D50V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(9Q34.13) MUTATED     3 337
  DEL PEAK 17(9Q34.13) WILD-TYPE   0 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(9Q34.13) MUTATED      3  337
  DEL PEAK 17(9Q34.13) WILD-TYPE    0  231
     clus
vv    DEL PEAK 17(9Q34.13) MUTATED DEL PEAK 17(9Q34.13) WILD-TYPE
  NO                             3                              0
  YES                          337                            231
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 17(9Q34.13) MUTATED    9 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                            9                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(9Q34.13) MUTATED                                  1     9
  DEL PEAK 17(9Q34.13) WILD-TYPE                                2     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(9Q34.13) MUTATED                          16
  DEL PEAK 17(9Q34.13) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 17(9Q34.13) MUTATED                                           1
  DEL PEAK 17(9Q34.13) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 17(9Q34.13) MUTATED     285
  DEL PEAK 17(9Q34.13) WILD-TYPE   190
D50V7, multiclass
                                           clus
vv                                          DEL PEAK 17(9Q34.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              285
                                           clus
vv                                          DEL PEAK 17(9Q34.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 17(9Q34.13) MUTATED     6 197
  DEL PEAK 17(9Q34.13) WILD-TYPE   4 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(9Q34.13) MUTATED      6  197
  DEL PEAK 17(9Q34.13) WILD-TYPE    4  128
                        clus
vv                       DEL PEAK 17(9Q34.13) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          197
                        clus
vv                       DEL PEAK 17(9Q34.13) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            128
[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    59  53
  DEL PEAK 18(10P15.3) WILD-TYPE 207 237
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           112                            444 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            53                            237 
$`DEL PEAK 18(10P15.3) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1351 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       40.24         1.81        65.46        44.32        33.67        76.57 
TCGA-04-1371 TCGA-04-1646 TCGA-04-1648 TCGA-09-0364 TCGA-09-0367 TCGA-09-2043 
       82.39        27.88        28.64        29.16        17.98         6.18 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2055 TCGA-10-0927 TCGA-10-0928 TCGA-10-0938 
       63.09        39.75        26.93        81.47        18.51        19.86 
TCGA-13-0714 TCGA-13-0761 TCGA-13-0766 TCGA-13-0799 TCGA-13-0889 TCGA-13-0890 
        6.21        34.06        21.40         7.79        61.84        67.99 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0905 TCGA-13-0908 TCGA-13-0921 TCGA-13-1404 
       57.47        56.15        47.84        44.84         4.64         6.61 
TCGA-13-1408 TCGA-13-1412 TCGA-13-1482 TCGA-13-1492 TCGA-13-1494 TCGA-13-1500 
        5.92         5.33        61.71        73.55        38.20        13.97 
TCGA-13-1510 TCGA-13-2057 TCGA-13-2065 TCGA-20-0996 TCGA-20-1684 TCGA-20-1687 
        2.56        14.24         8.75        72.20        19.10         2.66 
TCGA-23-1109 TCGA-23-1114 TCGA-23-1119 TCGA-23-1809 TCGA-23-2078 TCGA-23-2641 
       51.35        68.68       129.96         0.53        87.48         2.76 
TCGA-23-2643 TCGA-24-0975 TCGA-24-0979 TCGA-24-1416 TCGA-24-1423 TCGA-24-1425 
        4.70        21.80        41.56         6.38         6.25         5.95 
TCGA-24-1426 TCGA-24-1435 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 TCGA-24-1546 
        5.36        43.53       105.99         1.18        22.22        64.27 
TCGA-24-1558 TCGA-24-1567 TCGA-24-1842 TCGA-24-1844 TCGA-24-1849 TCGA-24-1850 
       19.53        17.23         8.32         3.72         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1927 TCGA-24-2019 TCGA-24-2024 TCGA-24-2027 
        9.80        22.68        16.44         4.87        58.16       109.71 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2293 TCGA-25-1313 TCGA-25-1323 TCGA-25-1625 
       64.01        57.07        16.64        26.96        12.00        18.02 
TCGA-25-1630 TCGA-25-1632 TCGA-25-2042 TCGA-25-2393 TCGA-25-2399 TCGA-25-2400 
        7.86        56.94        13.02        38.04        19.99        42.02 
TCGA-29-1688 TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1761 
       78.90        38.53        31.20        68.32         0.53        17.00 
TCGA-29-1764 TCGA-30-1714 TCGA-30-1855 TCGA-30-1891 TCGA-31-1946 TCGA-31-1959 
       62.93        38.07         2.47        30.05        30.18         2.20 
TCGA-36-1570 TCGA-36-2534 TCGA-36-2538 TCGA-36-2544 TCGA-36-2545 TCGA-42-2582 
       21.53        29.82        25.08        20.98        18.31        26.04 
TCGA-57-1992 TCGA-61-1736 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1907 
       29.00        48.79        43.69         1.45         8.42        31.30 
TCGA-61-2016 TCGA-61-2096 TCGA-61-2097 TCGA-61-2614 
        1.18        58.39        60.62         8.61 

$`DEL PEAK 18(10P15.3) WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       41.00        49.15         2.01        46.62        18.51        11.87 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 
       65.52        63.09        48.76        21.57        63.98        49.28 
TCGA-04-1361 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       32.52        71.47        56.55        41.59        19.99        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-09-0365 TCGA-09-0366 
       36.23        31.86        47.70        45.37         9.47        57.76 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       35.57         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
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-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
      112.41        71.11        20.94        12.46        54.31        25.91 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       33.24        32.28        11.70         3.91        35.44        35.80 
TCGA-10-0937 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 
       15.12        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 
       31.10        15.19        17.82        55.17         2.50        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0768 TCGA-13-0791 
       11.38        11.54        32.25        31.04         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0800 
       36.72        28.70        30.35        19.59         8.71         8.12 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 
        8.28         8.19        43.86        35.28        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 
       68.94       107.18        91.40        74.27        66.67        70.39 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       69.01        43.36        57.07        19.36        47.38        48.33 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.94        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 
       14.89        13.81         6.41         6.08        10.88         7.36 
TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
        6.05         6.84         4.70         4.21        54.64        87.06 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 
       29.42        98.04        20.68        22.39        70.82        82.88 
TCGA-13-1491 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 
       52.44        49.25         4.24        54.31        37.61        38.40 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2071 
        3.91         3.09        12.23         8.61        10.78         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 
       54.77         8.42        23.05        25.94        26.20        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
       25.38        16.70         2.93        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       15.39        26.83        31.76        49.41         8.81        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 
       18.90         2.24        54.51         3.22        31.20         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       33.30        86.01         4.27         6.38        39.09        33.47 
TCGA-23-1124 TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 
       58.13        24.95       115.89        91.66        77.00        49.84 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 TCGA-24-0980 TCGA-24-0982 
        4.50         7.63        19.66        11.64         7.66        22.32 
TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1418 
       54.12        63.55        47.41         6.31         7.82         7.99 
TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 
        7.86         0.76         6.02         4.83        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 
       19.17        18.67         8.55        72.92        12.46        45.14 
TCGA-24-1469 TCGA-24-1470 TCGA-24-1544 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        9.11         3.45        26.96        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        51.91        41.39        58.09        88.50        70.62 
TCGA-24-1557 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       39.88        44.09        45.50        47.70        25.87        10.26 
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-24-1924 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 
        4.37        11.28        30.21        11.05        81.11       152.02 
TCGA-24-2023 TCGA-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 
       44.84        34.82        14.43        53.95        18.48        28.18 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        36.16         0.79         0.36        47.54        31.63 
TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 
       70.45        44.61         0.82        67.36        36.23        33.11 
TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
        2.96        18.58        15.81         0.36        20.61         0.30 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 
       85.05        49.05         1.02         3.02        12.00        45.01 
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        44.71        47.18 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
      101.79         0.79        33.70        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        29.23        34.62        85.68        66.81 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1774 
       39.12        31.23        22.98        24.36        22.55        17.33 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 
       12.36        11.84        12.30        14.93         8.38         7.23 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 
        5.36        34.62        86.17        65.00        62.47        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ 
        4.90        42.25        11.84        11.47         9.76        21.04 
TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       51.91        36.26        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-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 
       48.79        45.57        18.77        22.49         6.71        42.51 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 
       44.12        28.77        29.10        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-36-2532 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 TCGA-36-2543 
       33.01        29.49        25.91        23.80        21.60         2.24 
TCGA-36-2547 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA 
       20.52        14.17         6.05        16.18        11.47         7.99 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 
       23.74         9.44        42.02         7.46        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-59-A5PD TCGA-61-1721 
       34.39         2.14         5.42        44.81        20.52        11.11 
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-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1741 
       31.79        28.47        44.84        35.80         2.43        33.67 
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-61-1911 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-61-1995 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-61-2009 TCGA-61-2012 TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 
       30.64        39.85        30.64        45.96        45.40         4.80 
TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 TCGA-61-2098 TCGA-61-2101 
        4.77        51.72        71.74        61.64        65.52        55.50 
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-61-2612 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         8.05 

  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 
                        129.96                         180.20 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        25.560                         28.735 
[1] "0.5 - 130.0 (25.6)" "0.3 - 180.2 (28.7)"
[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       1   444                2
D51V3, multiclass
                  clus
vv                 DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     113                            444
  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, continuous
D51V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(10P15.3) MUTATED     1 116
  DEL PEAK 18(10P15.3) WILD-TYPE   2 452
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      1  116
  DEL PEAK 18(10P15.3) WILD-TYPE    2  452
     clus
vv    DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  NO                             1                              2
  YES                          116                            452
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(10P15.3) MUTATED    2  4  0  0
  DEL PEAK 18(10P15.3) WILD-TYPE 12 22  5  3
D51V6, multiclass
    clus
vv   DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  R0                            2                             12
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(10P15.3) MUTATED                                  1     2
  DEL PEAK 18(10P15.3) WILD-TYPE                                2    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(10P15.3) MUTATED                           5
  DEL PEAK 18(10P15.3) WILD-TYPE                        27
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 18(10P15.3) MUTATED                                           1
  DEL PEAK 18(10P15.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 18(10P15.3) MUTATED      97
  DEL PEAK 18(10P15.3) WILD-TYPE   378
D51V7, multiclass
                                           clus
vv                                          DEL PEAK 18(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               97
                                           clus
vv                                          DEL PEAK 18(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                378
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(10P15.3) MUTATED     1  60
  DEL PEAK 18(10P15.3) WILD-TYPE   9 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      1   60
  DEL PEAK 18(10P15.3) WILD-TYPE    9  265
                        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                            265
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 19(10Q24.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(10Q24.2) MUTATED   128 116
  DEL PEAK 19(10Q24.2) WILD-TYPE 138 174
  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                           244                            312 
  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                           116                            174 
$`DEL PEAK 19(10Q24.2) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1342 TCGA-04-1343 TCGA-04-1364 TCGA-04-1367 
       40.24        41.00        18.51        11.87        33.67        71.47 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1654 
       38.37        29.10        48.89        28.64        64.64        47.70 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 
       57.76        17.98        35.57        41.62        57.60        61.87 
TCGA-09-1668 TCGA-09-1673 TCGA-09-1675 TCGA-09-2045 TCGA-09-2051 TCGA-09-2053 
       55.36         3.02        97.55        35.15        63.09        39.75 
TCGA-10-0931 TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0723 
       32.28        35.44        19.86         6.21        44.55        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0751 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
        2.73        12.39        55.17        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 
       31.04        21.40         8.45        38.93        36.72        30.35 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0807 TCGA-13-0885 
        7.79         8.12         8.28        43.86        13.61        91.40 
TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 
       66.67        61.84        69.01        43.36        57.47        56.15 
TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0910 TCGA-13-0911 
       57.07        19.36        47.38        48.33        37.08        27.72 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        13.81         4.64         6.41         6.08 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1410 TCGA-13-1483 TCGA-13-1488 
        6.61         7.36         5.92         4.70        29.42        70.82 
TCGA-13-1489 TCGA-13-1492 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       82.88        73.55        49.25         4.24        54.31        37.61 
TCGA-13-1501 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2057 
       32.84         4.77         4.18         2.56         3.09        14.24 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-20-0987 TCGA-20-1682 TCGA-20-1684 
       12.23        10.78         8.75        23.05        27.52        19.10 
TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 TCGA-23-1027 TCGA-23-1032 TCGA-23-1110 
        2.93         2.66        47.54        31.76         2.24        54.51 
TCGA-23-1111 TCGA-23-1114 TCGA-23-1117 TCGA-23-1119 TCGA-23-1121 TCGA-23-1122 
        3.22        68.68        33.30       129.96         6.38        39.09 
TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 
       33.47         0.53        24.95       115.89        77.00        49.84 
TCGA-23-2641 TCGA-24-0968 TCGA-24-0979 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 
        2.76        19.66        41.56        54.12        63.55         6.38 
TCGA-24-1417 TCGA-24-1418 TCGA-24-1423 TCGA-24-1425 TCGA-24-1430 TCGA-24-1431 
        7.82         7.99         6.25         5.95        28.37        19.17 
TCGA-24-1434 TCGA-24-1436 TCGA-24-1466 TCGA-24-1467 TCGA-24-1471 TCGA-24-1474 
       18.67         8.55        45.14       105.99         1.18        22.22 
TCGA-24-1544 TCGA-24-1552 TCGA-24-1556 TCGA-24-1557 TCGA-24-1563 TCGA-24-1604 
       26.96        41.39        70.62        39.88        47.70        88.37 
TCGA-24-1614 TCGA-24-1842 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1849 
       48.33         8.32         3.72         3.81        11.28         5.79 
TCGA-24-1850 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 TCGA-24-2024 TCGA-24-2026 
        5.52        16.44        11.05       152.02        58.16        34.82 
TCGA-24-2030 TCGA-24-2036 TCGA-24-2254 TCGA-24-2267 TCGA-24-2280 TCGA-24-2288 
       53.95        64.01        57.07        47.54        70.45         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       67.36        36.23        55.86        53.26         1.02        26.96 
TCGA-25-1320 TCGA-25-1329 TCGA-25-1631 TCGA-25-1632 TCGA-25-1635 TCGA-25-2042 
       36.95         2.96         0.30        56.94        51.22        13.02 
TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 TCGA-29-1696 
       19.99        42.02        26.99        47.18        38.53        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       31.20        68.32         0.53        16.90        18.67        59.67 
TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 
       41.98        34.62        17.00        66.81        62.93        39.12 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       22.98        24.36        17.33        12.36        11.84        12.30 
TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 TCGA-29-1785 TCGA-29-2427 TCGA-29-2429 
       14.93         8.38         5.36        34.62        62.47         4.90 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-31-1944 
       51.91         2.47        15.68        48.10        44.91        45.57 
TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 TCGA-36-1574 TCGA-36-1577 TCGA-36-1578 
       22.49         6.71         2.20        22.55        25.74        27.85 
TCGA-36-1581 TCGA-36-2532 TCGA-36-2534 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 
       24.69        29.49        29.82        21.60        18.31        20.52 
TCGA-36-2551 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2591 TCGA-57-1582 TCGA-57-1994 
       16.18         7.99        26.04        40.77        24.03        25.02 
TCGA-59-A5PD TCGA-61-1724 TCGA-61-1727 TCGA-61-1728 TCGA-61-1734 TCGA-61-1737 
       20.52        20.94        18.54        27.88        28.47        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-61-1903 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
       13.02        37.05        48.92        56.61        43.43        15.75 
TCGA-61-2000 TCGA-61-2008 TCGA-61-2012 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 
       14.50        30.64        30.64         4.77        51.72        71.74 
TCGA-61-2102 TCGA-61-2104 TCGA-61-2113 TCGA-OY-A56P 
        6.48        76.87        22.22        39.68 

$`DEL PEAK 19(10Q24.2) WILD-TYPE`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1346 TCGA-04-1347 
        1.81        49.15         2.01        46.62        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-04-1365 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-04-1530 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 
      119.08        84.20        55.43        27.88        36.23        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       45.37        29.16         9.47         9.99        38.43        89.33 
TCGA-09-1664 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2043 
       74.93        30.51        17.98         5.85         8.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2054 TCGA-09-2055 
        6.12         4.54       112.41        71.11        20.94        26.93 
TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0717 TCGA-13-0726 
       11.70         3.91        35.80        15.12        24.59        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0762 TCGA-13-0793 
       15.19        17.82         2.50        11.18        32.25        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 
       19.59         8.71         8.19        35.28        35.28        68.94 
TCGA-13-0884 TCGA-13-0886 TCGA-13-0888 TCGA-13-0890 TCGA-13-0905 TCGA-13-0906 
      107.18        74.27        70.39        67.99        47.84        44.94 
TCGA-13-0908 TCGA-13-0912 TCGA-13-0919 TCGA-13-1403 TCGA-13-1407 TCGA-13-1409 
       44.84        34.06        14.89        10.88         6.05         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 
        4.21         5.33        54.64        87.06        61.71        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1494 TCGA-13-1499 TCGA-13-1500 
       20.68        22.39        52.44        38.20        38.40        13.97 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1511 TCGA-13-2060 TCGA-13-2071 
       16.57         4.21         4.41         3.91         8.61         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 
       54.77         8.42        25.94        26.20        72.20        25.38 
TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 
       16.70        42.54        40.54        15.39        26.83        49.41 
TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 TCGA-23-1113 TCGA-23-1116 
        8.81        29.13        18.90        51.35        31.20         4.57 
TCGA-23-1118 TCGA-23-1120 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2643 
       86.01         4.27        58.13        87.48        91.66         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-24-1105 TCGA-24-1413 TCGA-24-1419 TCGA-24-1422 TCGA-24-1424 TCGA-24-1426 
       47.41         6.31         7.86         0.76         6.02         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1435 TCGA-24-1463 TCGA-24-1464 TCGA-24-1469 
        4.83        17.39        43.53        72.92        12.46         9.11 
TCGA-24-1470 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 
        3.45        57.40        64.27        16.21        56.58        41.06 
TCGA-24-1551 TCGA-24-1553 TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 
       51.91        58.09        88.50        19.53        44.09        45.50 
TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1616 TCGA-24-1843 
       25.87        10.26        17.23        90.15        38.24         3.48 
TCGA-24-1846 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1930 TCGA-24-2019 
        4.37         9.80        22.68        30.21        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-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       33.11        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1319 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 
       65.00        33.96         2.99        12.00        18.58        18.02 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 TCGA-25-1634 
       15.81         0.36        20.61         7.86        60.59        35.54 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 
       14.96        24.99        18.05        85.05        49.05         1.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 TCGA-25-2398 TCGA-25-2401 TCGA-25-2404 
       38.04         3.02        12.00        45.01         2.96        29.03 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1695 TCGA-29-1705 
       31.00        78.90        44.71       101.79         0.79        18.25 
TCGA-29-1710 TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1783 TCGA-29-2414 
       29.23        85.68        31.23        22.55         7.23        86.17 
TCGA-29-2425 TCGA-29-2428 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-2436 
       65.00        45.11        42.25        11.84        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       21.04        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-31-1946 TCGA-31-1950 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 
       30.18        18.77        42.51        44.12        28.77        29.10 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 
       21.53        22.85         8.55        30.08        24.23        35.05 
TCGA-36-2530 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 
       33.01        25.91        25.08        23.80         2.24        20.98 
TCGA-36-2548 TCGA-36-2549 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 
       14.17         6.05        11.47        23.74         9.44        42.02 
TCGA-42-2590 TCGA-42-2593 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        7.46         1.48        11.38        21.14         1.74        22.32 
TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 
       29.00        25.08       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-61-1740 
        8.09        31.43         4.34        31.79        48.79         2.43 
TCGA-61-1899 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 
        8.42         9.07        34.13        31.30        42.51        67.76 
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-61-2095 TCGA-61-2096 
        1.18        45.96        45.40         4.80        61.64        58.39 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2109 TCGA-61-2110 TCGA-61-2111 
       60.62        65.52        55.50        20.68        44.52       125.75 
TCGA-61-2612 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
        6.35        31.07         8.61        18.94         0.79         8.05 

  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                        152.02                         180.20 
  DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE 
                        28.870                         26.515 
[1] "0.3 - 152.0 (28.9)" "0.3 - 180.2 (26.5)"
[1] "hr=" "1.2"
D52V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 19(10Q24.2) MUTATED         1   243                1
  DEL PEAK 19(10Q24.2) WILD-TYPE       1   314                1
D52V3, multiclass
                  clus
vv                 DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     243                            314
  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"
D52V4, continuous
D52V5, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q24.2) MUTATED     2 248
  DEL PEAK 19(10Q24.2) WILD-TYPE   1 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q24.2) MUTATED      2  248
  DEL PEAK 19(10Q24.2) WILD-TYPE    1  320
     clus
vv    DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE
  NO                             2                              1
  YES                          248                            320
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 19(10Q24.2) MUTATED    4  8  1  1
  DEL PEAK 19(10Q24.2) WILD-TYPE 10 18  4  2
D52V6, multiclass
    clus
vv   DEL PEAK 19(10Q24.2) MUTATED DEL PEAK 19(10Q24.2) WILD-TYPE
  R0                            4                             10
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(10Q24.2) MUTATED                                  1    10
  DEL PEAK 19(10Q24.2) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(10Q24.2) MUTATED                          20
  DEL PEAK 19(10Q24.2) WILD-TYPE                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 19(10Q24.2) MUTATED                                           1
  DEL PEAK 19(10Q24.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 19(10Q24.2) MUTATED     206
  DEL PEAK 19(10Q24.2) WILD-TYPE   269
D52V7, multiclass
                                           clus
vv                                          DEL PEAK 19(10Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                           20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              206
                                           clus
vv                                          DEL PEAK 19(10Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                  8
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                269
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(10Q24.2) MUTATED     4 141
  DEL PEAK 19(10Q24.2) WILD-TYPE   6 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(10Q24.2) MUTATED      4  141
  DEL PEAK 19(10Q24.2) WILD-TYPE    6  184
                        clus
vv                       DEL PEAK 19(10Q24.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       DEL PEAK 19(10Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            184
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 20(11P15.5) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(11P15.5) MUTATED   175 158
  DEL PEAK 20(11P15.5) WILD-TYPE  91 132
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           333                            223 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                           158                            132 
$`DEL PEAK 20(11P15.5) MUTATED`
TCGA-04-1331 TCGA-04-1338 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1351 
       40.24        46.62        65.52        63.09        21.57        65.46 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       32.52        44.32        76.57        71.47        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1644 
       19.99        38.37       119.08        29.10        84.20        48.89 
TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 TCGA-04-1655 
       27.88        28.64        64.64        36.23        47.70        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1661 TCGA-09-1665 TCGA-09-1666 
       57.76        17.98        35.57        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-10-0926 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 
       12.46        25.91        18.51        33.24        32.28        15.12 
TCGA-13-0714 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0751 
        6.21        39.58         2.73        12.39        31.10        55.17 
TCGA-13-0755 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 
        2.50        11.38        11.54        32.25        31.04        21.40 
TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 
        8.45        36.72        28.70        30.35        19.59         8.71 
TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0883 TCGA-13-0885 
        8.28         8.19        43.86        35.28        68.94        91.40 
TCGA-13-0886 TCGA-13-0890 TCGA-13-0893 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 
       74.27        67.99        43.36        56.15        57.07        19.36 
TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 
       47.38        48.33        47.84        44.94        44.84        29.98 
TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1488 
        5.33        54.64        61.71        29.42        98.04        70.82 
TCGA-13-1489 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1500 TCGA-13-1501 
       82.88        38.20        49.25        54.31        13.97        32.84 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 TCGA-13-2059 TCGA-13-2065 
        4.21         4.41         4.77        14.24        12.23         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-1682 TCGA-20-1683 
        6.28        54.77         8.42        25.94        27.52        25.38 
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        42.54        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1110 
       26.83        31.76        49.41         8.81        18.90        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       31.20        68.68        33.30        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1124 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 
       39.09        58.13       115.89        87.48        91.66        77.00 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 
        2.76         4.70         4.50        19.66        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 
       53.95        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        32.02        51.06        34.98 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 
       12.00         2.96        18.02         0.36        20.61         7.86 
TCGA-25-1631 TCGA-25-1634 TCGA-25-1870 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
        0.30        35.54        14.96        18.05        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 
       47.18       101.79        38.53        31.20        18.67        59.67 
TCGA-29-1705 TCGA-29-1711 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       18.25        34.62        85.68        66.81        62.93        31.23 
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        11.84 
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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
        7.99        26.04        23.74         9.44        42.02         7.46 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
       40.77        24.03        21.14         1.74        29.00        25.08 
TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 
       22.32         9.40         5.42        44.81        20.52         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1734 
       20.94        31.43        18.54        27.88         4.34        28.47 
TCGA-61-1737 TCGA-61-1738 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 
       44.84        35.80        43.69         1.45         8.42         5.79 
TCGA-61-1901 TCGA-61-1903 TCGA-61-1904 TCGA-61-1906 TCGA-61-1910 TCGA-61-1913 
       11.41        13.02         9.07        34.13        37.05        48.92 
TCGA-61-1914 TCGA-61-1919 TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2018 
       56.61        38.17        17.98        39.85        30.64        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2102 TCGA-61-2109 
        4.80         4.77        51.72        71.74         6.48        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-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

$`DEL PEAK 20(11P15.5) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 TCGA-04-1343 
       41.00         1.81        49.15         2.01        18.51        11.87 
TCGA-04-1348 TCGA-04-1350 TCGA-04-1356 TCGA-04-1364 TCGA-04-1516 TCGA-04-1638 
       48.76        63.98        49.28        33.67        41.59        55.43 
TCGA-04-1652 TCGA-09-0364 TCGA-09-0365 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       31.86        29.16         9.47         9.99        89.33        74.93 
TCGA-09-1672 TCGA-09-1673 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 TCGA-09-2054 
        5.85         3.02         4.54        71.11        63.09        20.94 
TCGA-10-0925 TCGA-10-0927 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 
       54.31        81.47        11.70         3.91        35.44        35.80 
TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 
       19.86        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 
       34.06        38.93         7.79         8.12        35.28        13.61 
TCGA-13-0884 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 TCGA-13-0897 
      107.18        66.67        70.39        61.84        69.01        57.47 
TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0919 TCGA-13-1407 TCGA-13-1481 
       37.08        27.72        34.06        14.89         6.05        87.06 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 TCGA-13-1498 
       20.68        22.39        52.44        73.55         4.24        37.61 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       38.40        16.57         4.18         2.56         3.91         3.09 
TCGA-13-2060 TCGA-13-2061 TCGA-20-0987 TCGA-20-0991 TCGA-20-0996 TCGA-20-1684 
        8.61        10.78        23.05        26.20        72.20        19.10 
TCGA-23-1024 TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1116 
       15.39        29.13         2.24        51.35         3.22         4.57 
TCGA-23-1121 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2084 TCGA-24-0966 
        6.38        33.47         0.53        24.95        49.84         7.63 
TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 
       41.56         7.66        22.32         6.38         7.99         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1426 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        0.76         6.25         5.36        28.37        19.17        18.67 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1471 TCGA-24-1546 TCGA-24-1548 TCGA-24-1550 
       12.46       105.99         1.18        64.27        16.21        41.06 
TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1557 TCGA-24-1560 TCGA-24-1565 
       41.39        58.09        88.50        39.88        44.09        10.26 
TCGA-24-1603 TCGA-24-1842 TCGA-24-1844 TCGA-24-1850 TCGA-24-1928 TCGA-24-2020 
       90.15         8.32         3.72         5.52        11.05       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       44.84        58.16       109.71        28.18        64.01        44.52 
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-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1316 TCGA-25-1317 
       16.64        55.86        53.26         1.02        37.02         1.02 
TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1623 TCGA-25-1626 
       65.00        36.95        33.96         2.99        18.58        15.81 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 
       56.94        60.59        51.22        24.99        49.05         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 
       12.00        45.01        19.99        29.03        31.00        44.71 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1707 
        0.79        33.70        68.32         0.53        16.90        41.98 
TCGA-29-1710 TCGA-29-1761 TCGA-29-1766 TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 
       29.23        17.00        39.12        22.55        17.33        14.93 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2434 TCGA-29-2436 
       34.62        62.47        45.11         4.90        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1855 TCGA-30-1859 TCGA-30-1867 TCGA-30-1880 
       21.04        38.07         2.47        48.10         1.22        57.57 
TCGA-30-1892 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-36-1570 
       48.79        30.18        18.77        22.49        42.51        21.53 
TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 TCGA-36-1580 TCGA-36-2529 TCGA-36-2532 
       22.85         8.55        30.08        24.23        35.05        29.49 
TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-36-2551 TCGA-42-2593 TCGA-57-1583 
       23.80        20.98        14.17        16.18         1.48        11.38 
TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 
       22.32        25.02       180.20        80.12       116.12        34.39 
TCGA-59-2355 TCGA-61-1721 TCGA-61-1733 TCGA-61-1736 TCGA-61-1740 TCGA-61-1741 
        2.14        11.11        31.79        48.79         2.43        33.67 
TCGA-61-1907 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1995 
       31.30        42.51        67.76        43.43        15.75         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2016 TCGA-61-2017 
        5.52        14.50         4.01        30.64         1.18        45.96 
TCGA-61-2095 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       61.64        58.39        60.62        65.52        55.50        76.87 
TCGA-61-2110 
       44.52 

  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                        129.96                         180.20 
  DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE 
                         27.85                          29.03 
[1] "0.3 - 130.0 (27.9)" "0.5 - 180.2 (29.0)"
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 20(11P15.5) MUTATED         0   336                0
  DEL PEAK 20(11P15.5) WILD-TYPE       2   221                2
D53V3, multiclass
                  clus
vv                 DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     336                            221
  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"
D53V4, continuous
D53V5, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED     2 338
  DEL PEAK 20(11P15.5) WILD-TYPE   1 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED      2  338
  DEL PEAK 20(11P15.5) WILD-TYPE    1  230
     clus
vv    DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  NO                             2                              1
  YES                          338                            230
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 20(11P15.5) MUTATED   10 16  4  3
  DEL PEAK 20(11P15.5) WILD-TYPE  4 10  1  0
D53V6, multiclass
    clus
vv   DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
  R0                           10                              4
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(11P15.5) MUTATED                                  1    12
  DEL PEAK 20(11P15.5) WILD-TYPE                                2     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(11P15.5) MUTATED                          22
  DEL PEAK 20(11P15.5) WILD-TYPE                        10
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 20(11P15.5) MUTATED                                           1
  DEL PEAK 20(11P15.5) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 20(11P15.5) MUTATED     283
  DEL PEAK 20(11P15.5) WILD-TYPE   192
D53V7, multiclass
                                           clus
vv                                          DEL PEAK 20(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                               12
  BLACK OR AFRICAN AMERICAN                                           22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              283
                                           clus
vv                                          DEL PEAK 20(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                  6
  BLACK OR AFRICAN AMERICAN                                             10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                192
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(11P15.5) MUTATED     6 199
  DEL PEAK 20(11P15.5) WILD-TYPE   4 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(11P15.5) MUTATED      6  199
  DEL PEAK 20(11P15.5) WILD-TYPE    4  126
                        clus
vv                       DEL PEAK 20(11P15.5) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          199
                        clus
vv                       DEL PEAK 20(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            126
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 21(11Q25) MUTATION ANALYSIS
D54V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 21(11Q25) MUTATED    92 104
  DEL PEAK 21(11Q25) WILD-TYPE 174 186
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         196                          360 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                         104                          186 
$`DEL PEAK 21(11Q25) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1338 TCGA-04-1342 TCGA-04-1348 TCGA-04-1351 
       40.24         1.81        46.62        18.51        48.76        65.46 
TCGA-04-1356 TCGA-04-1361 TCGA-04-1514 TCGA-04-1516 TCGA-04-1530 TCGA-04-1536 
       49.28        32.52        56.55        41.59       119.08        29.10 
TCGA-04-1648 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 TCGA-09-0369 TCGA-09-1666 
       28.64        45.37        29.16        57.76        35.57        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-2044 TCGA-09-2050 
       61.87        30.51        17.98         3.02         6.12        71.11 
TCGA-09-2053 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 
       39.75        26.93        12.46        25.91        81.47        33.24 
TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       32.28        15.12        19.86        44.55        39.58         2.73 
TCGA-13-0730 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0768 
       17.82        11.18        11.38        11.54        32.25         8.45 
TCGA-13-0795 TCGA-13-0801 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 
       19.59         8.28        91.40        70.39        61.84        69.01 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0906 TCGA-13-0910 TCGA-13-0920 TCGA-13-0924 
       56.15        57.07        44.94        37.08        13.81         6.08 
TCGA-13-1409 TCGA-13-1411 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 
        6.84         4.21        61.71        29.42        22.39        82.88 
TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 TCGA-13-1501 TCGA-13-1510 TCGA-13-1512 
       38.20        49.25        54.31        32.84         2.56         3.09 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0991 
        8.61        10.78         8.75         6.28         8.42        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 TCGA-23-1022 TCGA-23-1028 TCGA-23-1113 
       27.52        25.38        19.10        42.54        49.41        31.20 
TCGA-23-1118 TCGA-23-1122 TCGA-23-2072 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 
       86.01        39.09        24.95        49.84         4.70         4.50 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1418 TCGA-24-1427 
       19.66        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        53.95 
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        51.06        34.98        36.95 
TCGA-25-1321 TCGA-25-1329 TCGA-25-1627 TCGA-25-1628 TCGA-25-1635 TCGA-25-1870 
       33.96         2.96         0.36        20.61        51.22        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 
       29.23        34.62        17.00        39.12        31.23        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        26.04        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-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       20.52        20.94        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1903 
       31.79        28.47        33.67        43.69         1.45        13.02 
TCGA-61-1904 TCGA-61-1910 TCGA-61-1911 TCGA-61-1918 TCGA-61-1919 TCGA-61-2012 
        9.07        37.05        42.51        15.75        38.17        30.64 
TCGA-61-2016 TCGA-61-2018 TCGA-61-2092 TCGA-61-2096 TCGA-61-2102 TCGA-61-2111 
        1.18        45.40        51.72        58.39         6.48       125.75 
TCGA-61-2113 TCGA-61-2612 TCGA-OY-A56Q TCGA-WR-A838 
       22.22         6.35        18.94         8.05 

$`DEL PEAK 21(11Q25) WILD-TYPE`
TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       41.00        49.15         2.01        11.87        65.52        63.09 
TCGA-04-1349 TCGA-04-1350 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       21.57        63.98        44.32        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1517 TCGA-04-1525 TCGA-04-1542 TCGA-04-1638 TCGA-04-1644 
       82.39        19.99        38.37        84.20        55.43        48.89 
TCGA-04-1646 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-09-0365 
       27.88        64.64        36.23        31.86        47.70         9.47 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       17.98         9.99        38.43        89.33        74.93        41.62 
TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 
       55.36         5.85         8.55        97.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2051 TCGA-09-2054 TCGA-10-0925 TCGA-10-0928 
        4.54       112.41        63.09        20.94        54.31        18.51 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-13-0714 TCGA-13-0717 
       11.70         3.91        35.44        35.80         6.21        24.59 
TCGA-13-0725 TCGA-13-0726 TCGA-13-0727 TCGA-13-0751 TCGA-13-0755 TCGA-13-0761 
       12.39        31.10        15.19        55.17         2.50        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       31.04        21.40        38.93        36.72        28.70        30.35 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 
        8.71         7.79         8.12         8.19        43.86        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 TCGA-13-0887 
       35.28        13.61        68.94       107.18        74.27        66.67 
TCGA-13-0890 TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       67.99        43.36        57.47        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       47.84        44.84        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       14.89         4.64         6.41        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.05         5.92         4.70         5.33        54.64        87.06 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1491 TCGA-13-1492 TCGA-13-1496 
       98.04        20.68        70.82        52.44        73.55         4.24 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 
       37.61        38.40        13.97        16.57         4.21         4.41 
TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-2059 TCGA-13-A5FT 
        4.77         4.18         3.91        14.24        12.23        54.77 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 
       23.05        25.94        72.20        16.70         2.93         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
       47.54        40.54        15.39        26.83        31.76         8.81 
TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       29.13        18.90         2.24        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         4.57        33.30       129.96         4.27         6.38 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2078 TCGA-23-2079 
       33.47        58.13         0.53       115.89        87.48        91.66 
TCGA-23-2081 TCGA-23-2641 TCGA-24-0966 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 
       77.00         2.76         7.63        21.80         7.66        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1419 
       63.55        47.41         6.31         6.38         7.82         7.86 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 
        0.76         6.25         6.02         5.95         5.36        17.39 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 TCGA-24-1435 TCGA-24-1436 TCGA-24-1467 
       28.37        19.17        18.67        43.53         8.55       105.99 
TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1545 TCGA-24-1548 TCGA-24-1549 
        3.45         1.18        22.22        57.40        16.21        56.58 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 
       41.06        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-24-1614 TCGA-24-1616 TCGA-24-1843 TCGA-24-1845 TCGA-24-1846 
       88.37        48.33        38.24         3.48         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1927 TCGA-24-1930 TCGA-24-2023 
       11.28         5.79         9.80        16.44        81.11        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 TCGA-24-2035 
       58.16        34.82       109.71        14.43        18.48        28.18 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 
       64.01        44.52         0.36        31.63        44.61         0.82 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-25-1312 TCGA-25-1314 TCGA-25-1316 
       67.36        36.23        33.11         1.02        32.02        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1322 TCGA-25-1323 TCGA-25-1623 TCGA-25-1625 
        1.02        65.00         2.99        12.00        18.58        18.02 
TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       15.81         7.86         0.30        56.94        60.59        35.54 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2396 TCGA-25-2397 
       18.05        85.05        13.02        49.05         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-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       26.99        44.71        47.18       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 
       33.70        31.20        68.32         0.53        16.90        18.67 
TCGA-29-1707 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1769 TCGA-29-1771 
       41.98        85.68        66.81        62.93        22.98        22.55 
TCGA-29-1774 TCGA-29-1776 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 TCGA-29-1785 
       17.33        11.84         8.38         7.23         5.36        34.62 
TCGA-29-2425 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 
       65.00        62.47         4.90        42.25        11.84         9.76 
TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 
       21.04        36.26        15.68         0.26        48.10        44.91 
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-31-1950 TCGA-31-1951 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 
       45.57        18.77        22.49        42.51         2.20        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-1577 
       29.10        21.53        22.55         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       27.85        29.49        29.82        25.91        25.08        23.80 
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-3P-A9WA TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 
       11.47         7.99        23.74         9.44         7.46        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       24.03        11.38        21.14        22.32        29.00        25.08 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 
       80.12        22.32         9.40         5.42        44.81        11.11 
TCGA-61-1722 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 
        8.09        48.79        44.84        35.80         2.43         8.42 
TCGA-61-1900 TCGA-61-1901 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 
        5.79        11.41        34.13        31.30        48.92        56.61 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 
       67.76        43.43         2.01         5.52        14.50        17.98 
TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 
        4.01        30.64        39.85        45.96         4.80         4.77 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 
       71.74        61.64        60.62        65.52        55.50        76.87 
TCGA-61-2109 TCGA-61-2110 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO 
       20.68        44.52        31.07         8.61        39.68         0.79 

  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                        0.36                         0.26 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                      180.20                       129.96 
  DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE 
                      29.130                       27.355 
[1] "0.4 - 180.2 (29.1)" "0.3 - 130.0 (27.4)"
[1] "hr=" "1"  
D54V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 21(11Q25) MUTATED         1   195                2
  DEL PEAK 21(11Q25) WILD-TYPE       1   362                0
D54V3, multiclass
                  clus
vv                 DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  OMENTUM                                   1                            1
  OVARY                                   195                          362
  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"
D54V4, continuous
D54V5, binary
                              cls
clus                             0   1
  DEL PEAK 21(11Q25) MUTATED     2 198
  DEL PEAK 21(11Q25) WILD-TYPE   1 370
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED      2  198
  DEL PEAK 21(11Q25) WILD-TYPE    1  370
     clus
vv    DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  NO                           2                            1
  YES                        198                          370
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 21(11Q25) MUTATED    5  6  2  1
  DEL PEAK 21(11Q25) WILD-TYPE  9 20  3  2
D54V6, multiclass
    clus
vv   DEL PEAK 21(11Q25) MUTATED DEL PEAK 21(11Q25) WILD-TYPE
  R0                          5                            9
  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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(11Q25) MUTATED                                  1     5
  DEL PEAK 21(11Q25) WILD-TYPE                                2    13
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(11Q25) MUTATED                          11
  DEL PEAK 21(11Q25) WILD-TYPE                        21
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(11Q25) MUTATED                                           0   172
  DEL PEAK 21(11Q25) WILD-TYPE                                         1   303
D54V7, multiclass
                                           clus
vv                                          DEL PEAK 21(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              5
  BLACK OR AFRICAN AMERICAN                                         11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                            172
                                           clus
vv                                          DEL PEAK 21(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               13
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              303
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                              cls
clus                             0   1
  DEL PEAK 21(11Q25) MUTATED     7 112
  DEL PEAK 21(11Q25) WILD-TYPE   3 213
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(11Q25) MUTATED      7  112
  DEL PEAK 21(11Q25) WILD-TYPE    3  213
                        clus
vv                       DEL PEAK 21(11Q25) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                        112
                        clus
vv                       DEL PEAK 21(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          213
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 22(12Q24.33) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 22(12Q24.33) MUTATED    95 112
  DEL PEAK 22(12Q24.33) WILD-TYPE 171 178
  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                            207                             349 
  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                            112                             178 
$`DEL PEAK 22(12Q24.33) MUTATED`
TCGA-04-1335 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1371 TCGA-04-1517 
        1.81        65.46        49.28        32.52        82.39        19.99 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1646 TCGA-04-1651 TCGA-04-1654 
       29.10        84.20        55.43        27.88        36.23        47.70 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 
       17.98         9.99        38.43        89.33        57.60        61.87 
TCGA-09-1668 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2051 TCGA-09-2056 
       55.36         8.55         6.12        35.15        63.09        12.46 
TCGA-10-0925 TCGA-10-0928 TCGA-10-0937 TCGA-13-0720 TCGA-13-0724 TCGA-13-0725 
       54.31        18.51        15.12        44.55         2.73        12.39 
TCGA-13-0726 TCGA-13-0751 TCGA-13-0755 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 
       31.10        55.17         2.50        11.38        34.06        32.25 
TCGA-13-0793 TCGA-13-0797 TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 
       28.70         8.71         8.28        43.86        35.28        13.61 
TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 
       68.94       107.18        91.40        66.67        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
       43.36        57.47        47.84        44.84        37.08        27.72 
TCGA-13-0913 TCGA-13-0919 TCGA-13-0923 TCGA-13-1404 TCGA-13-1405 TCGA-13-1408 
       29.98        14.89         6.41         6.61         7.36         5.92 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1488 
        4.70         4.21         5.33        61.71        29.42        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1501 TCGA-13-1507 
       82.88        52.44        73.55        38.20        32.84         4.77 
TCGA-13-1509 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-A5FT TCGA-13-A5FU 
        4.18         3.09        12.23        10.78        54.77         8.42 
TCGA-20-0987 TCGA-20-1687 TCGA-23-1022 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       23.05         2.66        42.54        26.83        31.76        49.41 
TCGA-23-1110 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 
       54.51        33.30        86.01         4.27        39.09        58.13 
TCGA-23-2077 TCGA-23-2078 TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 
      115.89        87.48         4.50        11.64        21.80         7.66 
TCGA-24-0982 TCGA-24-1104 TCGA-24-1105 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
       22.32        63.55        47.41         7.99         0.76         6.25 
TCGA-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 
        5.95         4.83        17.39        19.17         8.55        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1550 TCGA-24-1557 
       45.14         9.11         3.45         1.18        41.06        39.88 
TCGA-24-1562 TCGA-24-1567 TCGA-24-1614 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 
       45.50        17.23        48.33         3.72         4.37        11.28 
TCGA-24-1849 TCGA-24-1924 TCGA-24-1927 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 
        5.79        30.21        16.44        81.11       152.02        44.84 
TCGA-24-2026 TCGA-24-2027 TCGA-24-2035 TCGA-24-2254 TCGA-24-2267 TCGA-24-2280 
       34.82       109.71        28.18        57.07        47.54        70.45 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-25-1313 TCGA-25-1318 TCGA-25-1321 
       36.23        16.64        55.86        26.96        34.98        33.96 
TCGA-25-1625 TCGA-25-1630 TCGA-25-1632 TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 
       18.02         7.86        56.94        18.05        13.02        49.05 
TCGA-25-2393 TCGA-25-2397 TCGA-25-2400 TCGA-25-2401 TCGA-25-2409 TCGA-29-1688 
       38.04        12.00        42.02         2.96        26.99        78.90 
TCGA-29-1691 TCGA-29-1694 TCGA-29-1701 TCGA-29-1703 TCGA-29-1711 TCGA-29-1761 
       47.18        38.53        16.90        59.67        34.62        17.00 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1770 TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 
       66.81        31.23        24.36        12.36        11.84        12.30 
TCGA-29-1781 TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2432 
        8.38         5.36        86.17        65.00        62.47        11.84 
TCGA-30-1853 TCGA-30-1857 TCGA-30-1860 TCGA-30-1861 TCGA-30-1891 TCGA-31-1956 
       36.26         0.26        44.91        34.78        30.05        44.12 
TCGA-31-1959 TCGA-36-1574 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 
        2.20        22.55        29.82        25.91        25.08        21.60 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2589 TCGA-42-2591 
        2.24        20.98         6.05         7.99        42.02        40.77 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-59-2350 TCGA-61-1722 TCGA-61-1724 
       24.03        21.14         1.74        22.32         8.09        20.94 
TCGA-61-1727 TCGA-61-1738 TCGA-61-1740 TCGA-61-1895 TCGA-61-1901 TCGA-61-1903 
       18.54        35.80         2.43         1.45        11.41        13.02 
TCGA-61-1904 TCGA-61-1917 TCGA-61-1919 TCGA-61-2008 TCGA-61-2018 TCGA-61-2096 
        9.07        43.43        38.17        30.64        45.40        58.39 
TCGA-61-2102 TCGA-61-2109 TCGA-61-2612 
        6.48        20.68         6.35 

$`DEL PEAK 22(12Q24.33) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
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-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1514 TCGA-04-1516 
       44.32        33.67        76.57        71.47        56.55        41.59 
TCGA-04-1525 TCGA-04-1530 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 
       38.37       119.08        48.89        28.64        64.64        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1664 
       45.37        29.16         9.47        57.76        35.57        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-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 
       26.93        25.91        81.47        33.24        32.28        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
        3.91        35.44        35.80        19.86         6.21        24.59 
TCGA-13-0723 TCGA-13-0727 TCGA-13-0730 TCGA-13-0757 TCGA-13-0760 TCGA-13-0764 
       39.58        15.19        17.82        11.18        11.54        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 
       21.40         8.45        38.93        36.72        30.35        19.59 
TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 TCGA-13-0886 TCGA-13-0888 
        7.79         8.12         8.19        35.28        74.27        70.39 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       67.99        56.15        57.07        19.36        47.38        48.33 
TCGA-13-0906 TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 TCGA-13-0921 TCGA-13-0924 
       44.94        34.06        21.17        13.81         4.64         6.08 
TCGA-13-1403 TCGA-13-1407 TCGA-13-1409 TCGA-13-1477 TCGA-13-1481 TCGA-13-1484 
       10.88         6.05         6.84        54.64        87.06        98.04 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       20.68        22.39        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 
       38.40        13.97        16.57         4.21         4.41         2.56 
TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-20-0990 
        3.91        14.24         8.61         8.75         6.28        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         2.24        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 
        4.57       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-24-0968 TCGA-24-0979 TCGA-24-1103 TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 
       19.66        41.56        54.12         6.31         6.38         7.82 
TCGA-24-1419 TCGA-24-1424 TCGA-24-1426 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        7.86         6.02         5.36        28.37        18.67        43.53 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       12.46       105.99        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1553 TCGA-24-1555 
       16.21        56.58        51.91        41.39        58.09        88.50 
TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1565 
       70.62        19.53        44.09        47.70        25.87        10.26 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       90.15        88.37        38.24         8.32         3.48         3.81 
TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1928 TCGA-24-2019 TCGA-24-2024 
        5.52         9.80        22.68        11.05         4.87        58.16 
TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2038 TCGA-24-2260 
       14.43        53.95        18.48        64.01        44.52        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2288 TCGA-24-2289 
        0.79         0.36        31.63        44.61         0.82        67.36 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       33.11        53.26         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
        1.02        65.00        36.95         2.99        12.00         2.96 
TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1633 
       18.58        15.81         0.36        20.61         0.30        60.59 
TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2392 
       35.54        51.22        14.96        24.99        85.05         1.02 
TCGA-25-2396 TCGA-25-2398 TCGA-25-2399 TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 
        3.02        45.01        19.99        29.03        31.00        44.71 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
      101.79         0.79        33.70        31.20        68.32         0.53 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1762 TCGA-29-1764 
       18.67        18.25        41.98        29.23        85.68        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1771 TCGA-29-1774 TCGA-29-1778 TCGA-29-1783 
       39.12        22.98        22.55        17.33        14.93         7.23 
TCGA-29-1785 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 TCGA-29-2436 
       34.62        45.11         4.90        42.25        11.47         9.76 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 
       21.04        38.07        51.91         2.47        15.68        48.10 
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-31-1955 
       45.57        30.18        18.77        22.49         6.71        42.51 
TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1575 TCGA-36-1576 
       28.77        29.10        21.53        22.85         8.55        30.08 
TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 
       25.74        27.85        24.23        24.69        35.05        33.01 
TCGA-36-2532 TCGA-36-2540 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
       29.49        23.80        18.31        20.52        14.17        16.18 
TCGA-36-2552 TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2593 
       11.47        26.04        23.74         9.44         7.46         1.48 
TCGA-57-1583 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       11.38        22.32        29.00        25.08        25.02       180.20 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 
       44.81        20.52        11.11        31.43        27.88         4.34 
TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1741 TCGA-61-1743 
       31.79        28.47        48.79        44.84        33.67        43.69 
TCGA-61-1899 TCGA-61-1900 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1911 
        8.42         5.79        34.13        31.30        37.05        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-1998 
       48.92        56.61        67.76        15.75         2.01         5.52 
TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       14.50        17.98         4.01        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2094 TCGA-61-2095 
       45.96         4.80         4.77        51.72        71.74        61.64 
TCGA-61-2097 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 
       60.62        65.52        55.50        76.87        44.52       125.75 
TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
       22.22        31.07         8.61        39.68        18.94         0.79 
TCGA-WR-A838 
        8.05 

  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                           0.26                            0.30 
  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                         152.02                          180.20 
  DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE 
                          29.10                           27.52 
[1] "0.3 - 152.0 (29.1)" "0.3 - 180.2 (27.5)"
[1] "hr=" "1"  
D55V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 22(12Q24.33) MUTATED         2   208                0
  DEL PEAK 22(12Q24.33) WILD-TYPE       0   349                2
D55V3, multiclass
                  clus
vv                 DEL PEAK 22(12Q24.33) MUTATED
  OMENTUM                                      2
  OVARY                                      208
  PERITONEUM OVARY                             0
                  clus
vv                 DEL PEAK 22(12Q24.33) WILD-TYPE
  OMENTUM                                        0
  OVARY                                        349
  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"
D55V4, continuous
D55V5, binary
                                 cls
clus                                0   1
  DEL PEAK 22(12Q24.33) MUTATED     0 214
  DEL PEAK 22(12Q24.33) WILD-TYPE   3 354
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(12Q24.33) MUTATED      0  214
  DEL PEAK 22(12Q24.33) WILD-TYPE    3  354
     clus
vv    DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE
  NO                              0                               3
  YES                           214                             354
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 22(12Q24.33) MUTATED    2 13  1  2
  DEL PEAK 22(12Q24.33) WILD-TYPE 12 13  4  1
D55V6, multiclass
    clus
vv   DEL PEAK 22(12Q24.33) MUTATED DEL PEAK 22(12Q24.33) WILD-TYPE
  R0                             2                              12
  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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(12Q24.33) MUTATED                                  1     8
  DEL PEAK 22(12Q24.33) WILD-TYPE                                2    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(12Q24.33) MUTATED                          14
  DEL PEAK 22(12Q24.33) WILD-TYPE                        18
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 22(12Q24.33) MUTATED                                           1
  DEL PEAK 22(12Q24.33) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 22(12Q24.33) MUTATED     175
  DEL PEAK 22(12Q24.33) WILD-TYPE   300
D55V7, multiclass
                                           clus
vv                                          DEL PEAK 22(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 8
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               175
                                           clus
vv                                          DEL PEAK 22(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        2
  ASIAN                                                                  10
  BLACK OR AFRICAN AMERICAN                                              18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                 300
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                                 cls
clus                                0   1
  DEL PEAK 22(12Q24.33) MUTATED     7 110
  DEL PEAK 22(12Q24.33) WILD-TYPE   3 215
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 22(12Q24.33) MUTATED      7  110
  DEL PEAK 22(12Q24.33) WILD-TYPE    3  215
                        clus
vv                       DEL PEAK 22(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           110
                        clus
vv                       DEL PEAK 22(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             215
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 23(13Q14.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(13Q14.2) MUTATED   169 178
  DEL PEAK 23(13Q14.2) WILD-TYPE  97 112
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           347                            209 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                           178                            112 
$`DEL PEAK 23(13Q14.2) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1349 TCGA-04-1361 TCGA-04-1365 TCGA-04-1367 
       11.87        63.09        21.57        32.52        76.57        71.47 
TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        41.59        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 
       55.43        27.88        28.64        64.64        36.23        31.86 
TCGA-04-1655 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1665 
       45.37        57.76        35.57         9.99        38.43        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2048 TCGA-09-2050 TCGA-09-2051 
        3.02         8.55         6.12         4.54        71.11        63.09 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       20.94        26.93        54.31        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 
       32.28        35.80        15.12        19.86        24.59        44.55 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 
        2.73        12.39        31.10        17.82        55.17         2.50 
TCGA-13-0758 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0793 
       11.38        31.04        21.40         8.45        36.72        28.70 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 
       19.59         8.71         7.79         8.12         8.19        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 
       66.67        70.39        67.99        69.01        43.36        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       44.94        21.17        14.89        13.81         6.41         6.08 
TCGA-13-1404 TCGA-13-1409 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
        6.61         6.84        87.06        61.71        29.42        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1497 
       70.82        82.88        73.55        38.20        49.25        54.31 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 
       38.40        13.97        32.84        16.57         4.21         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        2.56         3.91        14.24         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 
        6.28        54.77         8.42        26.20        27.52        19.10 
TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 
       16.70         2.66        47.54        40.54        15.39        31.76 
TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1032 TCGA-23-1110 TCGA-23-1114 
       49.41         8.81        18.90         2.24        54.51        68.68 
TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1122 TCGA-23-1123 
        4.57        86.01       129.96         4.27        39.09        33.47 
TCGA-23-1809 TCGA-23-2077 TCGA-23-2081 TCGA-23-2084 TCGA-23-2641 TCGA-23-2643 
        0.53       115.89        77.00        49.84         2.76         4.70 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0975 TCGA-24-0979 TCGA-24-0980 TCGA-24-1103 
        7.63        19.66        21.80        41.56         7.66        54.12 
TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 TCGA-24-1417 TCGA-24-1419 TCGA-24-1424 
       63.55        47.41         6.31         7.82         7.86         6.02 
TCGA-24-1425 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 
        5.95         5.36        17.39        28.37        18.67        43.53 
TCGA-24-1464 TCGA-24-1469 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       12.46         9.11        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 
       16.21        56.58        51.91        41.39        88.50        70.62 
TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 TCGA-24-1567 
       39.88        19.53        44.09        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-24-1844 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-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2019 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        11.05         4.87       152.02        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2027 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 
       58.16        34.82       109.71        64.01        57.07        36.16 
TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 TCGA-24-2289 TCGA-24-2290 
        0.79         0.36        47.54        70.45        67.36        36.23 
TCGA-25-1313 TCGA-25-1315 TCGA-25-1318 TCGA-25-1319 TCGA-25-1321 TCGA-25-1329 
       26.96        51.06        34.98        65.00        33.96         2.96 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        0.36        20.61         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1878 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       51.22        85.05        49.05         1.02        38.04         3.02 
TCGA-25-2397 TCGA-25-2399 TCGA-25-2400 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
       12.00        19.99        42.02         2.96        29.03        26.99 
TCGA-29-1688 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 TCGA-29-1697 
       78.90        47.18       101.79        38.53        33.70        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 
       68.32         0.53        16.90        18.67        59.67        41.98 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 
       85.68        66.81        62.93        39.12        31.23        22.55 
TCGA-29-1775 TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1784 
       12.36        11.84        12.30        14.93         8.38         5.36 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-30-1860 
       86.17        62.47        42.25        11.84        11.47        44.91 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1891 TCGA-31-1946 TCGA-31-1950 TCGA-31-1953 
       34.78        36.62        30.05        30.18        18.77         6.71 
TCGA-31-1955 TCGA-31-1959 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 
       42.51         2.20        29.10        21.53        22.85        22.55 
TCGA-36-1575 TCGA-36-1578 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2542 
        8.55        27.85        24.69        35.05        29.49        21.60 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2590 
        2.24        18.31        20.52         7.99        26.04         7.46 
TCGA-42-2591 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-59-2350 TCGA-59-2351 
       40.77        21.14         1.74        29.00        22.32       116.12 
TCGA-59-2352 TCGA-59-2354 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 
        9.40        34.39        44.81        20.52         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 
       22.22         6.35         8.61        39.68        18.94 

$`DEL PEAK 23(13Q14.2) WILD-TYPE`
TCGA-04-1337 TCGA-04-1346 TCGA-04-1348 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
        2.01        65.52        48.76        63.98        65.46        49.28 
TCGA-04-1362 TCGA-04-1364 TCGA-04-1371 TCGA-04-1517 TCGA-04-1644 TCGA-04-1654 
       44.32        33.67        82.39        19.99        48.89        47.70 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 TCGA-09-1675 
       29.16         9.47        17.98        89.33        74.93        97.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2049 TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 
        6.18        35.15       112.41        39.75        12.46        25.91 
TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-13-0714 TCGA-13-0723 TCGA-13-0727 
       11.70         3.91        35.44         6.21        39.58        15.19 
TCGA-13-0757 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0791 TCGA-13-0794 
       11.18        11.54        34.06        32.25        38.93        30.35 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0889 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 
        8.28        43.86        61.84        44.84        37.08        27.72 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0921 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 
       34.06        29.98         4.64        10.88         7.36         6.05 
TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1484 
        5.92         4.70         4.21         5.33        54.64        98.04 
TCGA-13-1485 TCGA-13-1491 TCGA-13-1496 TCGA-13-1498 TCGA-13-1506 TCGA-13-1507 
       20.68        52.44         4.24        37.61         4.41         4.77 
TCGA-13-1512 TCGA-13-2059 TCGA-20-0987 TCGA-20-0990 TCGA-20-0996 TCGA-20-1683 
        3.09        12.23        23.05        25.94        72.20        25.38 
TCGA-20-1686 TCGA-23-1022 TCGA-23-1026 TCGA-23-1030 TCGA-23-1109 TCGA-23-1111 
        2.93        42.54        26.83        29.13        51.35         3.22 
TCGA-23-1113 TCGA-23-1117 TCGA-23-1121 TCGA-23-1124 TCGA-23-2072 TCGA-23-2078 
       31.20        33.30         6.38        58.13        24.95        87.48 
TCGA-23-2079 TCGA-23-2645 TCGA-24-0970 TCGA-24-0982 TCGA-24-1416 TCGA-24-1418 
       91.66         4.50        11.64        22.32         6.38         7.99 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1427 TCGA-24-1431 TCGA-24-1436 TCGA-24-1463 
        0.76         6.25         4.83        19.17         8.55        72.92 
TCGA-24-1466 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1550 TCGA-24-1553 
       45.14       105.99         3.45         1.18        41.06        58.09 
TCGA-24-1562 TCGA-24-1565 TCGA-24-1849 TCGA-24-1923 TCGA-24-1930 TCGA-24-2029 
       45.50        10.26         5.79        22.68        81.11        14.43 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2038 TCGA-24-2271 TCGA-24-2281 
       53.95        18.48        28.18        44.52        31.63        44.61 
TCGA-24-2288 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
        0.82        16.64        33.11        55.86        53.26         1.02 
TCGA-25-1314 TCGA-25-1316 TCGA-25-1317 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       32.02        37.02         1.02        36.95         2.99        12.00 
TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1870 TCGA-25-1871 
       18.58        18.02        15.81         7.86        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2398 TCGA-25-2408 TCGA-29-1690 TCGA-29-1695 
       18.05        13.02        45.01        31.00        44.71         0.79 
TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1769 TCGA-29-1770 
       18.25        29.23        34.62        17.00        22.98        24.36 
TCGA-29-1774 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
       17.33         7.23        34.62        65.00        45.11         4.90 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
        9.76        21.04        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 
       15.68         0.26        48.10         6.12         1.22        57.57 
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-36-1576 TCGA-36-1577 TCGA-36-1580 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 
       30.08        25.74        24.23        33.01        29.82        25.91 
TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2548 TCGA-36-2549 TCGA-36-2551 
       25.08        23.80        20.98        14.17         6.05        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2593 TCGA-57-1582 
       11.47        23.74         9.44        42.02         1.48        24.03 
TCGA-57-1583 TCGA-57-1586 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 
       11.38        22.32        25.08        25.02       180.20        80.12 
TCGA-59-2355 TCGA-59-2363 TCGA-61-1721 TCGA-61-1728 TCGA-61-1741 TCGA-61-1900 
        2.14         5.42        11.11        27.88        33.67         5.79 
TCGA-61-1910 TCGA-61-1911 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2003 
       37.05        42.51        43.43        15.75        14.50         4.01 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2098 
       39.85        45.96        51.72        61.64        58.39        65.52 
TCGA-61-2101 TCGA-61-2109 TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       55.50        20.68        31.07         0.79         8.05 

  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                        152.02                         180.20 
  DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE 
                         29.49                          25.08 
[1] "0.3 - 152.0 (29.5)" "0.3 - 180.2 (25.1)"
[1] "hr=" "1.2"
D56V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 23(13Q14.2) MUTATED         1   348                2
  DEL PEAK 23(13Q14.2) WILD-TYPE       1   209                0
D56V3, multiclass
                  clus
vv                 DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     348                            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"
D56V4, continuous
D56V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED     1 357
  DEL PEAK 23(13Q14.2) WILD-TYPE   2 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED      1  357
  DEL PEAK 23(13Q14.2) WILD-TYPE    2  211
     clus
vv    DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  NO                             1                              2
  YES                          357                            211
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 23(13Q14.2) MUTATED    8 10  2  3
  DEL PEAK 23(13Q14.2) WILD-TYPE  6 16  3  0
D56V6, multiclass
    clus
vv   DEL PEAK 23(13Q14.2) MUTATED DEL PEAK 23(13Q14.2) WILD-TYPE
  R0                            8                              6
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(13Q14.2) MUTATED                                  1    10
  DEL PEAK 23(13Q14.2) WILD-TYPE                                2     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(13Q14.2) MUTATED                          25
  DEL PEAK 23(13Q14.2) WILD-TYPE                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(13Q14.2) MUTATED                                           0
  DEL PEAK 23(13Q14.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 23(13Q14.2) MUTATED     299
  DEL PEAK 23(13Q14.2) WILD-TYPE   176
D56V7, multiclass
                                           clus
vv                                          DEL PEAK 23(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                               10
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              299
                                           clus
vv                                          DEL PEAK 23(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                  8
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                176
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(13Q14.2) MUTATED     7 196
  DEL PEAK 23(13Q14.2) WILD-TYPE   3 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(13Q14.2) MUTATED      7  196
  DEL PEAK 23(13Q14.2) WILD-TYPE    3  129
                        clus
vv                       DEL PEAK 23(13Q14.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          196
                        clus
vv                       DEL PEAK 23(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            129
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 24(14Q23.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(14Q23.3) MUTATED   137 156
  DEL PEAK 24(14Q23.3) WILD-TYPE 129 134
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           293                            263 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                           156                            134 
$`DEL PEAK 24(14Q23.3) MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 
       41.00         1.81         2.01        46.62        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 
       63.09        48.76        65.46        49.28        32.52        44.32 
TCGA-04-1364 TCGA-04-1365 TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 
       33.67        76.57        82.39        41.59        38.37       119.08 
TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 TCGA-04-1654 
       84.20        55.43        28.64        64.64        36.23        47.70 
TCGA-04-1655 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1666 TCGA-09-1667 
       45.37        35.57         9.99        38.43        57.60        61.87 
TCGA-09-1668 TCGA-09-1670 TCGA-09-1672 TCGA-09-1675 TCGA-09-2048 TCGA-09-2050 
       55.36        17.98         5.85        97.55         4.54        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 
       63.09        39.75        20.94        12.46        54.31        25.91 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0935 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       18.51        32.28        35.44        19.86         6.21        24.59 
TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 
       44.55        39.58         2.73        31.10        15.19        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 TCGA-13-0764 
       55.17        11.18        11.38        11.54        34.06        31.04 
TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 
       21.40        38.93        36.72        30.35        19.59         7.79 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
        8.28        43.86       107.18        91.40        74.27        66.67 
TCGA-13-0888 TCGA-13-0891 TCGA-13-0893 TCGA-13-0906 TCGA-13-0913 TCGA-13-0919 
       70.39        69.01        43.36        44.94        29.98        14.89 
TCGA-13-0921 TCGA-13-0923 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1411 
        4.64         6.41         7.36         6.05         5.92         4.21 
TCGA-13-1481 TCGA-13-1482 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       87.06        61.71        22.39        70.82        82.88        52.44 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1501 
       38.20         4.24        54.31        37.61        38.40        32.84 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1507 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
       16.57         4.21         4.77         2.56         3.09        12.23 
TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FU TCGA-20-1683 
        8.61        10.78         8.75         6.28         8.42        25.38 
TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 TCGA-23-1021 TCGA-23-1024 TCGA-23-1026 
       19.10        16.70         2.66        47.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 
       31.76        49.41        29.13        51.35        54.51         3.22 
TCGA-23-1114 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
       68.68        33.30        86.01       129.96        39.09        33.47 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2081 TCGA-23-2643 TCGA-23-2645 
        0.53        24.95       115.89        77.00         4.70         4.50 
TCGA-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
       19.66        11.64        21.80        41.56        22.32        63.55 
TCGA-24-1105 TCGA-24-1417 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1425 
       47.41         7.82         0.76         6.25         6.02         5.95 
TCGA-24-1427 TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 
        4.83        19.17        18.67         8.55        72.92        12.46 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       45.14         9.11         3.45         1.18        22.22        26.96 
TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1551 TCGA-24-1552 TCGA-24-1556 
       64.27        16.21        56.58        51.91        41.39        70.62 
TCGA-24-1557 TCGA-24-1564 TCGA-24-1565 TCGA-24-1604 TCGA-24-1614 TCGA-24-1843 
       39.88        25.87        10.26        88.37        48.33         3.48 
TCGA-24-1845 TCGA-24-1846 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
        3.81         4.37        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2023 TCGA-24-2024 TCGA-24-2026 TCGA-24-2029 TCGA-24-2254 
        4.87        44.84        58.16        34.82        14.43        57.07 
TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2288 TCGA-24-2295 TCGA-24-2298 
       36.16         0.36        47.54         0.82        33.11        53.26 
TCGA-25-1313 TCGA-25-1320 TCGA-25-1321 TCGA-25-1626 TCGA-25-1630 TCGA-25-1631 
       26.96        36.95        33.96        15.81         7.86         0.30 
TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       56.94        35.54        51.22        14.96        24.99        18.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       13.02        49.05         1.02        38.04         3.02        12.00 
TCGA-25-2400 TCGA-25-2404 TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       42.02        29.03        47.18       101.79        38.53         0.79 
TCGA-29-1698 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 
       68.32        18.25        41.98        29.23        17.00        85.68 
TCGA-29-1763 TCGA-29-1766 TCGA-29-1771 TCGA-29-1776 TCGA-29-1777 TCGA-29-1784 
       66.81        39.12        22.55        11.84        12.30         5.36 
TCGA-29-1785 TCGA-29-2427 TCGA-29-2434 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       34.62        62.47        11.47        51.91         2.47        15.68 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1861 TCGA-30-1867 TCGA-30-1887 TCGA-30-1891 
       48.10        44.91        34.78         1.22        24.26        30.05 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 TCGA-31-1953 TCGA-31-1959 
       45.57        30.18        18.77        22.49         6.71         2.20 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1576 TCGA-36-2534 TCGA-36-2537 
       22.85        22.55         8.55        30.08        29.82        25.91 
TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
       25.08        21.60         2.24        20.52        14.17        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2589 TCGA-42-2591 TCGA-42-2593 TCGA-57-1992 
       11.47        23.74        42.02        40.77         1.48        29.00 
TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 TCGA-59-2351 TCGA-59-2372 TCGA-59-A5PD 
       25.08        25.02       180.20       116.12        44.81        20.52 
TCGA-61-1724 TCGA-61-1727 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1741 
       20.94        18.54        31.79        28.47        48.79        33.67 
TCGA-61-1743 TCGA-61-1895 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 
       43.69         1.45        11.41         9.07        34.13        31.30 
TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-2000 TCGA-61-2009 TCGA-61-2018 
       67.76        43.43        15.75        14.50        39.85        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2097 TCGA-61-2102 TCGA-61-2109 
        4.80         4.77        51.72        60.62         6.48        20.68 
TCGA-61-2111 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO 
      125.75         8.61        39.68        18.94         0.79 

$`DEL PEAK 24(14Q23.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1342 TCGA-04-1349 TCGA-04-1350 TCGA-04-1367 
       40.24        49.15        18.51        21.57        63.98        71.47 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1536 TCGA-04-1644 TCGA-04-1646 TCGA-04-1652 
       56.55        19.99        29.10        48.89        27.88        31.86 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1662 TCGA-09-1664 
       29.16         9.47        57.76        17.98        89.33        74.93 
TCGA-09-1665 TCGA-09-1669 TCGA-09-1673 TCGA-09-1674 TCGA-09-2043 TCGA-09-2044 
       41.62        30.51         3.02         8.55         6.18         6.12 
TCGA-09-2045 TCGA-09-2049 TCGA-09-2055 TCGA-10-0927 TCGA-10-0930 TCGA-10-0933 
       35.15       112.41        26.93        81.47        33.24        11.70 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-13-0725 TCGA-13-0755 TCGA-13-0762 
        3.91        35.80        15.12        12.39         2.50        32.25 
TCGA-13-0768 TCGA-13-0793 TCGA-13-0797 TCGA-13-0800 TCGA-13-0802 TCGA-13-0804 
        8.45        28.70         8.71         8.12         8.19        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0889 TCGA-13-0890 TCGA-13-0897 
       35.28        13.61        68.94        61.84        67.99        57.47 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       56.15        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0920 
       44.84        37.08        27.72        34.06        21.17        13.81 
TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 TCGA-13-1410 TCGA-13-1412 
        6.08        10.88         6.61         6.84         4.70         5.33 
TCGA-13-1477 TCGA-13-1483 TCGA-13-1484 TCGA-13-1485 TCGA-13-1492 TCGA-13-1495 
       54.64        29.42        98.04        20.68        73.55        49.25 
TCGA-13-1500 TCGA-13-1506 TCGA-13-1509 TCGA-13-1511 TCGA-13-2057 TCGA-13-A5FT 
       13.97         4.41         4.18         3.91        14.24        54.77 
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 
       42.54        40.54         8.81        18.90         2.24        31.20 
TCGA-23-1116 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 
        4.57         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        53.95        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 
       32.02        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1627 
        2.99        12.00         2.96        18.58        18.02         0.36 
TCGA-25-1628 TCGA-25-1633 TCGA-25-1878 TCGA-25-2398 TCGA-25-2399 TCGA-25-2401 
       20.61        60.59        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        44.71        33.70        31.20 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1711 TCGA-29-1764 
        0.53        16.90        18.67        59.67        34.62        62.93 
TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 
       31.23        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         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       42.25        11.84         9.76        21.04        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-3P-A9WA TCGA-42-2582 TCGA-42-2588 
       20.98        18.31         6.05         7.99        26.04         9.44 
TCGA-42-2590 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 
        7.46        24.03        11.38        21.14         1.74        22.32 
TCGA-59-2349 TCGA-59-2350 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       80.12        22.32         9.40        34.39         2.14         5.42 
TCGA-61-1721 TCGA-61-1722 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1737 
       11.11         8.09        31.43        27.88         4.34        44.84 
TCGA-61-1738 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 TCGA-61-1910 
       35.80         2.43         8.42         5.79        13.02        37.05 
TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 
       42.51        48.92        56.61        38.17         2.01         5.52 
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-61-2094 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-61-2110 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 TCGA-WR-A838 
       44.52        22.22         6.35        31.07         8.05 

  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                        180.20                         152.02 
  DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE 
                         29.03                          27.72 
[1] "0.3 - 180.2 (29.0)" "0.3 - 152.0 (27.7)"
[1] "hr=" "1"  
D57V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 24(14Q23.3) MUTATED         0   296                1
  DEL PEAK 24(14Q23.3) WILD-TYPE       2   261                1
D57V3, multiclass
                  clus
vv                 DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  OMENTUM                                     0                              2
  OVARY                                     296                            261
  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"
D57V4, continuous
D57V5, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED     0 301
  DEL PEAK 24(14Q23.3) WILD-TYPE   3 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED      0  301
  DEL PEAK 24(14Q23.3) WILD-TYPE    3  267
     clus
vv    DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  NO                             0                              3
  YES                          301                            267
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 24(14Q23.3) MUTATED    7 10  4  1
  DEL PEAK 24(14Q23.3) WILD-TYPE  7 16  1  2
D57V6, multiclass
    clus
vv   DEL PEAK 24(14Q23.3) MUTATED DEL PEAK 24(14Q23.3) WILD-TYPE
  R0                            7                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(14Q23.3) MUTATED                                  3     7
  DEL PEAK 24(14Q23.3) WILD-TYPE                                0    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(14Q23.3) MUTATED                          18
  DEL PEAK 24(14Q23.3) WILD-TYPE                        14
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(14Q23.3) MUTATED                                           0
  DEL PEAK 24(14Q23.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 24(14Q23.3) MUTATED     251
  DEL PEAK 24(14Q23.3) WILD-TYPE   224
D57V7, multiclass
                                           clus
vv                                          DEL PEAK 24(14Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              251
                                           clus
vv                                          DEL PEAK 24(14Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       0
  ASIAN                                                                 11
  BLACK OR AFRICAN AMERICAN                                             14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                224
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(14Q23.3) MUTATED     8 172
  DEL PEAK 24(14Q23.3) WILD-TYPE   2 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(14Q23.3) MUTATED      8  172
  DEL PEAK 24(14Q23.3) WILD-TYPE    2  153
                        clus
vv                       DEL PEAK 24(14Q23.3) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          172
                        clus
vv                       DEL PEAK 24(14Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 25(15Q11.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(15Q11.2) MUTATED   135 153
  DEL PEAK 25(15Q11.2) WILD-TYPE 131 137
  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                           288                            268 
  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                           153                            137 
$`DEL PEAK 25(15Q11.2) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 
       40.24        49.15        18.51        11.87        65.52        63.09 
TCGA-04-1350 TCGA-04-1364 TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 
       63.98        33.67        82.39        56.55        19.99        38.37 
TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1652 
       29.10        84.20        27.88        28.64        64.64        31.86 
TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 
       45.37        29.16         9.47        38.43        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-1674 TCGA-09-2050 TCGA-09-2051 
       30.51        17.98         3.02         8.55        71.11        63.09 
TCGA-09-2053 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 TCGA-10-0935 
       39.75        12.46        25.91        81.47        33.24        35.44 
TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0730 
       35.80        24.59        39.58         2.73        12.39        17.82 
TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0764 TCGA-13-0792 
       55.17        11.18        11.38        11.54        31.04        36.72 
TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
       28.70        30.35        19.59         8.28         8.19        43.86 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 
       35.28        13.61        68.94       107.18        91.40        66.67 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0899 TCGA-13-0904 TCGA-13-0910 TCGA-13-0920 
       67.99        69.01        56.15        48.33        37.08        13.81 
TCGA-13-0921 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
        4.64         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
        4.70         4.21        61.71        98.04        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       82.88        52.44        38.20         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 
       38.40        16.57         4.41         4.77         4.18         2.56 
TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 
       12.23        10.78         8.75         8.42        25.94        26.20 
TCGA-20-1682 TCGA-20-1683 TCGA-20-1686 TCGA-23-1022 TCGA-23-1030 TCGA-23-1031 
       27.52        25.38         2.93        42.54        29.13        18.90 
TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.24        51.35        54.51        31.20        68.68         4.57 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2084 
       39.09        33.47         0.53        24.95       115.89        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0979 TCGA-24-0982 
        2.76         4.70         4.50        19.66        41.56        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-24-1424 TCGA-24-1426 TCGA-24-1428 TCGA-24-1430 
        0.76         6.25         6.02         5.36        17.39        28.37 
TCGA-24-1431 TCGA-24-1434 TCGA-24-1436 TCGA-24-1463 TCGA-24-1466 TCGA-24-1467 
       19.17        18.67         8.55        72.92        45.14       105.99 
TCGA-24-1469 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 TCGA-24-1549 TCGA-24-1552 
        9.11         1.18        26.96        16.21        56.58        41.39 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1564 TCGA-24-1603 TCGA-24-1614 TCGA-24-1616 
       58.09        39.88        25.87        90.15        48.33        38.24 
TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1847 TCGA-24-1850 
        8.32         3.48         3.72         3.81        11.28         5.52 
TCGA-24-1923 TCGA-24-1927 TCGA-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2026 
       22.68        16.44        81.11         4.87       152.02        34.82 
TCGA-24-2030 TCGA-24-2033 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2288 
       53.95        18.48        57.07        36.16         0.79         0.82 
TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1313 
       36.23        16.64        55.86        53.26         1.02        26.96 
TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 
       32.02        51.06        37.02        65.00        36.95        33.96 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 
       12.00         2.96        18.58         0.36        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1871 TCGA-25-1877 
       56.94        60.59        35.54        51.22        24.99        18.05 
TCGA-25-2393 TCGA-29-1691 TCGA-29-1693 TCGA-29-1695 TCGA-29-1697 TCGA-29-1698 
       38.04        47.18       101.79         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 
        0.53        16.90        59.67        18.25        41.98        29.23 
TCGA-29-1761 TCGA-29-1763 TCGA-29-1766 TCGA-29-1769 TCGA-29-1774 TCGA-29-1777 
       17.00        66.81        39.12        22.98        17.33        12.30 
TCGA-29-1783 TCGA-29-1784 TCGA-29-2425 TCGA-29-2428 TCGA-29-2432 TCGA-30-1714 
        7.23         5.36        65.00        45.11        11.84        38.07 
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-30-1866 TCGA-30-1867 TCGA-30-1887 TCGA-30-1892 TCGA-31-1950 TCGA-31-1951 
       36.62         1.22        24.26        48.79        18.77        22.49 
TCGA-31-1953 TCGA-31-1959 TCGA-36-1575 TCGA-36-1577 TCGA-36-1581 TCGA-36-2529 
        6.71         2.20         8.55        25.74        24.69        35.05 
TCGA-36-2534 TCGA-36-2542 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
       29.82        21.60        18.31        20.52        14.17        16.18 
TCGA-42-2587 TCGA-42-2589 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       23.74        42.02         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2363 
       25.02       180.20        22.32       116.12         9.40         5.42 
TCGA-61-1728 TCGA-61-1733 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 
       27.88        31.79        28.47        48.79        44.84        35.80 
TCGA-61-1740 TCGA-61-1741 TCGA-61-1901 TCGA-61-1904 TCGA-61-1906 TCGA-61-1911 
        2.43        33.67        11.41         9.07        34.13        42.51 
TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1919 TCGA-61-2003 TCGA-61-2008 
       48.92        56.61        43.43        38.17         4.01        30.64 
TCGA-61-2012 TCGA-61-2087 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2098 
       30.64         4.80        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 

$`DEL PEAK 25(15Q11.2) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1338 TCGA-04-1348 TCGA-04-1349 
       41.00         1.81         2.01        46.62        48.76        21.57 
TCGA-04-1351 TCGA-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1365 TCGA-04-1367 
       65.46        49.28        32.52        44.32        76.57        71.47 
TCGA-04-1516 TCGA-04-1530 TCGA-04-1638 TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 
       41.59       119.08        55.43        48.89        36.23        47.70 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 
       57.76        17.98        35.57         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-10-0925 
       35.15         4.54       112.41        20.94        26.93        54.31 
TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 
       18.51        32.28        11.70         3.91        15.12        19.86 
TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 TCGA-13-0727 TCGA-13-0755 TCGA-13-0761 
        6.21        44.55        31.10        15.19         2.50        34.06 
TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0797 TCGA-13-0799 
       32.25        21.40         8.45        38.93         8.71         7.79 
TCGA-13-0800 TCGA-13-0804 TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0893 
        8.12        35.28        74.27        70.39        61.84        43.36 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       57.47        57.07        19.36        47.38        47.84        44.94 
TCGA-13-0908 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.84        27.72        34.06        29.98        21.17        14.89 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1412 TCGA-13-1477 TCGA-13-1481 
        6.41         6.08        10.88         5.33        54.64        87.06 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 TCGA-13-1495 TCGA-13-1500 TCGA-13-1501 
       29.42        20.68        73.55        49.25        13.97        32.84 
TCGA-13-1505 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2071 
        4.21         3.91         3.09        14.24         8.61         6.28 
TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       54.77        23.05        72.20        19.10        16.70         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        40.54        15.39        26.83        31.76        49.41 
TCGA-23-1029 TCGA-23-1111 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
        8.81         3.22        33.30        86.01       129.96         4.27 
TCGA-23-1121 TCGA-23-1124 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 
        6.38        58.13        87.48        91.66        77.00         7.63 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0980 TCGA-24-1104 TCGA-24-1417 TCGA-24-1425 
       11.64        21.80         7.66        63.55         7.82         5.95 
TCGA-24-1427 TCGA-24-1435 TCGA-24-1464 TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 
        4.83        43.53        12.46         3.45        22.22        57.40 
TCGA-24-1546 TCGA-24-1550 TCGA-24-1551 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 
       64.27        41.06        51.91        88.50        70.62        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 
       44.09        45.50        47.70        10.26        17.23        88.37 
TCGA-24-1846 TCGA-24-1849 TCGA-24-1920 TCGA-24-1924 TCGA-24-1928 TCGA-24-2023 
        4.37         5.79         9.80        30.21        11.05        44.84 
TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       58.16       109.71        14.43        28.18        64.01        44.52 
TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 TCGA-24-2280 TCGA-24-2281 TCGA-24-2289 
        0.36        47.54        31.63        70.45        44.61        67.36 
TCGA-24-2295 TCGA-25-1317 TCGA-25-1318 TCGA-25-1322 TCGA-25-1625 TCGA-25-1626 
       33.11         1.02        34.98         2.99        18.02        15.81 
TCGA-25-1630 TCGA-25-1870 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
        7.86        14.96        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-29-1694 
       29.03        31.00        26.99        78.90        44.71        38.53 
TCGA-29-1696 TCGA-29-1702 TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1768 
       33.70        18.67        34.62        85.68        62.93        31.23 
TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1776 TCGA-29-1778 TCGA-29-1781 
       24.36        22.55        12.36        11.84        14.93         8.38 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2434 
       34.62        86.17        62.47         4.90        42.25        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 TCGA-30-1857 TCGA-30-1862 TCGA-30-1880 
        9.76        21.04        36.26         0.26         6.12        57.57 
TCGA-30-1891 TCGA-31-1944 TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 TCGA-36-1568 
       30.05        45.57        30.18        42.51        44.12        28.77 
TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 TCGA-36-1578 
       29.10        21.53        22.85        22.55        30.08        27.85 
TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 
       24.23        33.01        29.49        25.91        25.08        23.80 
TCGA-36-2543 TCGA-36-2544 TCGA-36-2549 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
        2.24        20.98         6.05        11.47         7.99        26.04 
TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
        9.44         7.46        40.77         1.48        24.03        11.38 
TCGA-57-1584 TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD 
       21.14        80.12        34.39         2.14        44.81        20.52 
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 
       51.72        61.64         0.79         8.05 

  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                        180.20                         129.96 
  DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE 
                        28.420                         27.785 
[1] "0.3 - 180.2 (28.4)" "0.3 - 130.0 (27.8)"
[1] "hr=" "1"  
D58V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 25(15Q11.2) MUTATED         2   286                2
  DEL PEAK 25(15Q11.2) WILD-TYPE       0   271                0
D58V3, multiclass
                  clus
vv                 DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     286                            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"
D58V4, continuous
D58V5, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q11.2) MUTATED     3 292
  DEL PEAK 25(15Q11.2) WILD-TYPE   0 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q11.2) MUTATED      3  292
  DEL PEAK 25(15Q11.2) WILD-TYPE    0  276
     clus
vv    DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE
  NO                             3                              0
  YES                          292                            276
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 25(15Q11.2) MUTATED    5 14  2  1
  DEL PEAK 25(15Q11.2) WILD-TYPE  9 12  3  2
D58V6, multiclass
    clus
vv   DEL PEAK 25(15Q11.2) MUTATED DEL PEAK 25(15Q11.2) WILD-TYPE
  R0                            5                              9
  R1                           14                             12
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(15Q11.2) MUTATED                                  0     9
  DEL PEAK 25(15Q11.2) WILD-TYPE                                3     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(15Q11.2) MUTATED                          15
  DEL PEAK 25(15Q11.2) WILD-TYPE                        17
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(15Q11.2) MUTATED                                           0
  DEL PEAK 25(15Q11.2) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 25(15Q11.2) MUTATED     254
  DEL PEAK 25(15Q11.2) WILD-TYPE   221
D58V7, multiclass
                                           clus
vv                                          DEL PEAK 25(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              254
                                           clus
vv                                          DEL PEAK 25(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                221
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(15Q11.2) MUTATED     6 167
  DEL PEAK 25(15Q11.2) WILD-TYPE   4 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(15Q11.2) MUTATED      6  167
  DEL PEAK 25(15Q11.2) WILD-TYPE    4  158
                        clus
vv                       DEL PEAK 25(15Q11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          167
                        clus
vv                       DEL PEAK 25(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            158
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 26(15Q15.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(15Q15.1) MUTATED   163 186
  DEL PEAK 26(15Q15.1) WILD-TYPE 103 104
  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                           349                            207 
  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                           186                            104 
$`DEL PEAK 26(15Q15.1) MUTATED`
TCGA-04-1331 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 TCGA-04-1346 
       40.24        49.15        46.62        18.51        11.87        65.52 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 
       63.98        49.28        44.32        82.39        56.55        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-04-1648 TCGA-04-1649 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       28.64        64.64        31.86        45.37        29.16         9.47 
TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 
       17.98         9.99        38.43        61.87        55.36        30.51 
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-09-2054 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       39.75        20.94        12.46        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0935 TCGA-10-0936 TCGA-13-0717 TCGA-13-0723 
       18.51        33.24        35.44        35.80        24.59        39.58 
TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 
        2.73        12.39        15.19        17.82        55.17        11.18 
TCGA-13-0758 TCGA-13-0760 TCGA-13-0762 TCGA-13-0764 TCGA-13-0793 TCGA-13-0795 
       11.38        11.54        32.25        31.04        28.70        19.59 
TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 
        8.71         8.12         8.28         8.19        43.86        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 
       13.61        68.94       107.18        91.40        66.67        70.39 
TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0904 
       67.99        69.01        43.36        57.47        56.15        48.33 
TCGA-13-0905 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0921 
       47.84        37.08        27.72        34.06        21.17         4.64 
TCGA-13-0923 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.41         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
        4.21        87.06        61.71        98.04        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       82.88        52.44        38.20        49.25         4.24        54.31 
TCGA-13-1499 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        32.84        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1510 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        4.18         2.56        14.24        12.23        10.78         8.75 
TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 TCGA-20-1684 
        8.42        25.94        26.20        27.52        25.38        19.10 
TCGA-20-1686 TCGA-23-1022 TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 
        2.93        42.54        18.90         2.24        51.35        54.51 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 
       31.20        68.68         4.57        86.01       129.96        39.09 
TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2084 
       33.47        58.13         0.53        24.95       115.89        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 TCGA-24-0970 TCGA-24-0979 
        2.76         4.70         4.50        19.66        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        19.17        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        53.95        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        32.02        51.06        37.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
        0.36        20.61         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1877 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2397 
       51.22        18.05         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        47.18       101.79         0.79        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
        0.53        16.90        18.67        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       29.23        34.62        17.00        85.68        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1774 TCGA-29-1775 TCGA-29-1777 
       39.12        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 
       11.84        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 
       18.94 

$`DEL PEAK 26(15Q15.1) WILD-TYPE`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1337 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
       41.00         1.81         2.01        63.09        48.76        21.57 
TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1638 
       65.46        32.52        33.67        76.57        71.47        55.43 
TCGA-04-1644 TCGA-04-1651 TCGA-04-1654 TCGA-09-0366 TCGA-09-0369 TCGA-09-1662 
       48.89        36.23        47.70        57.76        35.57        89.33 
TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 TCGA-09-1672 TCGA-09-1673 TCGA-09-1675 
       74.93        41.62        57.60         5.85         3.02        97.55 
TCGA-09-2043 TCGA-09-2045 TCGA-09-2048 TCGA-09-2055 TCGA-10-0931 TCGA-10-0933 
        6.18        35.15         4.54        26.93        32.28        11.70 
TCGA-10-0934 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0726 
        3.91        15.12        19.86         6.21        44.55        31.10 
TCGA-13-0755 TCGA-13-0761 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 
        2.50        34.06        21.40         8.45        38.93        36.72 
TCGA-13-0794 TCGA-13-0799 TCGA-13-0804 TCGA-13-0886 TCGA-13-0889 TCGA-13-0900 
       30.35         7.79        35.28        74.27        61.84        57.07 
TCGA-13-0901 TCGA-13-0903 TCGA-13-0906 TCGA-13-0908 TCGA-13-0913 TCGA-13-0919 
       19.36        47.38        44.94        44.84        29.98        14.89 
TCGA-13-0920 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1412 TCGA-13-1477 
       13.81         6.08        10.88         6.61         5.33        54.64 
TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 TCGA-13-1498 TCGA-13-1500 TCGA-13-1511 
       29.42        20.68        73.55        37.61        13.97         3.91 
TCGA-13-1512 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 
        3.09         8.61         6.28        54.77        23.05        72.20 
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-23-1111 TCGA-23-1117 
       31.76        49.41         8.81        29.13         3.22        33.30 
TCGA-23-1120 TCGA-23-1121 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-24-0966 
        4.27         6.38        87.48        91.66        77.00         7.63 
TCGA-24-0975 TCGA-24-0980 TCGA-24-1104 TCGA-24-1427 TCGA-24-1464 TCGA-24-1467 
       21.80         7.66        63.55         4.83        12.46       105.99 
TCGA-24-1470 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1551 TCGA-24-1553 
        3.45        22.22        57.40        64.27        51.91        58.09 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 
       88.50        19.53        44.09        45.50        47.70        10.26 
TCGA-24-1604 TCGA-24-1849 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2033 
       88.37         5.79        58.16       109.71        14.43        18.48 
TCGA-24-2036 TCGA-24-2038 TCGA-24-2262 TCGA-24-2271 TCGA-24-2281 TCGA-24-2289 
       64.01        44.52         0.36        31.63        44.61        67.36 
TCGA-25-1317 TCGA-25-1625 TCGA-25-1626 TCGA-25-1630 TCGA-25-1870 TCGA-25-1871 
        1.02        18.02        15.81         7.86        14.96        24.99 
TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 
       85.05        13.02        49.05        45.01        19.99        42.02 
TCGA-25-2401 TCGA-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1690 TCGA-29-1694 
        2.96        31.00        26.99        78.90        44.71        38.53 
TCGA-29-1696 TCGA-29-1768 TCGA-29-1771 TCGA-29-1776 TCGA-29-1781 TCGA-29-1785 
       33.70        31.23        22.55        11.84         8.38        34.62 
TCGA-29-2427 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 
       62.47         4.90        42.25         9.76        21.04        36.26 
TCGA-30-1862 TCGA-30-1880 TCGA-31-1944 TCGA-31-1946 TCGA-31-1955 TCGA-31-1956 
        6.12        57.57        45.57        30.18        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-36-1578 TCGA-36-1580 TCGA-36-2530 TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 
       27.85        24.23        33.01        29.49        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA 
       23.80        21.60        20.98        20.52         6.05         7.99 
TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-42-2590 TCGA-42-2591 TCGA-57-1584 
       26.04        23.74         9.44         7.46        40.77        21.14 
TCGA-59-2349 TCGA-59-2354 TCGA-59-2355 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1721 
       80.12        34.39         2.14        44.81        20.52        11.11 
TCGA-61-1722 TCGA-61-1725 TCGA-61-1730 TCGA-61-1899 TCGA-61-1901 TCGA-61-1903 
        8.09        31.43         4.34         8.42        11.41        13.02 
TCGA-61-1910 TCGA-61-1915 TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 
       37.05        67.76        15.75         2.01        14.50        17.98 
TCGA-61-2009 TCGA-61-2017 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 TCGA-61-2109 
       39.85        45.96         4.77        51.72        61.64        20.68 
TCGA-61-2613 TCGA-VG-A8LO TCGA-WR-A838 
       31.07         0.79         8.05 

  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                          0.26                           0.36 
  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                        180.20                         109.71 
  DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE 
                         27.88                          28.77 
[1] "0.3 - 180.2 (27.9)" "0.4 - 109.7 (28.8)"
[1] "hr=" "1"  
D59V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 26(15Q15.1) MUTATED         2   349                2
  DEL PEAK 26(15Q15.1) WILD-TYPE       0   208                0
D59V3, multiclass
                  clus
vv                 DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     349                            208
  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"
D59V4, continuous
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q15.1) MUTATED     3 356
  DEL PEAK 26(15Q15.1) WILD-TYPE   0 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q15.1) MUTATED      3  356
  DEL PEAK 26(15Q15.1) WILD-TYPE    0  212
     clus
vv    DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE
  NO                             3                              0
  YES                          356                            212
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 26(15Q15.1) MUTATED    7 13  3  1
  DEL PEAK 26(15Q15.1) WILD-TYPE  7 13  2  2
D59V6, multiclass
    clus
vv   DEL PEAK 26(15Q15.1) MUTATED DEL PEAK 26(15Q15.1) WILD-TYPE
  R0                            7                              7
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(15Q15.1) MUTATED                                  2     9
  DEL PEAK 26(15Q15.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(15Q15.1) MUTATED                          20
  DEL PEAK 26(15Q15.1) WILD-TYPE                        12
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 26(15Q15.1) MUTATED                                           1
  DEL PEAK 26(15Q15.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 26(15Q15.1) MUTATED     305
  DEL PEAK 26(15Q15.1) WILD-TYPE   170
D59V7, multiclass
                                           clus
vv                                          DEL PEAK 26(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              305
                                           clus
vv                                          DEL PEAK 26(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                170
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(15Q15.1) MUTATED     8 197
  DEL PEAK 26(15Q15.1) WILD-TYPE   2 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(15Q15.1) MUTATED      8  197
  DEL PEAK 26(15Q15.1) WILD-TYPE    2  128
                        clus
vv                       DEL PEAK 26(15Q15.1) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          197
                        clus
vv                       DEL PEAK 26(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 27(16P13.3) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(16P13.3) MUTATED   149 151
  DEL PEAK 27(16P13.3) WILD-TYPE 117 139
  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                           300                            256 
  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                           151                            139 
$`DEL PEAK 27(16P13.3) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1343 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 
       11.87        48.76        21.57        63.98        49.28        44.32 
TCGA-04-1364 TCGA-04-1367 TCGA-04-1516 TCGA-04-1517 TCGA-04-1536 TCGA-04-1638 
       33.67        71.47        41.59        19.99        29.10        55.43 
TCGA-04-1644 TCGA-04-1649 TCGA-04-1654 TCGA-09-0367 TCGA-09-1659 TCGA-09-1666 
       48.89        64.64        47.70        17.98         9.99        57.60 
TCGA-09-1667 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 TCGA-09-2043 TCGA-09-2044 
       61.87        30.51        17.98         3.02         6.18         6.12 
TCGA-09-2045 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0935 
       35.15        71.11        39.75        20.94        26.93        35.44 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0717 TCGA-13-0720 TCGA-13-0724 TCGA-13-0727 
       15.12        19.86        24.59        44.55         2.73        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0764 TCGA-13-0766 
       17.82        55.17        11.18        11.38        31.04        21.40 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 
       38.93        28.70        30.35        19.59         7.79         8.12 
TCGA-13-0801 TCGA-13-0803 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
        8.28        43.86        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0891 TCGA-13-0893 
       91.40        74.27        66.67        61.84        69.01        43.36 
TCGA-13-0899 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 TCGA-13-0910 
       56.15        47.38        48.33        47.84        44.94        37.08 
TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       34.06        29.98        21.17        13.81         6.41         6.08 
TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1481 TCGA-13-1484 
        7.36         6.05         5.92         4.70        87.06        98.04 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1500 TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 
       54.31        37.61        13.97        32.84         4.41         4.77 
TCGA-13-1509 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
        4.18         3.09        14.24        10.78         8.75        54.77 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1683 TCGA-23-1024 TCGA-23-1028 TCGA-23-1029 
       25.94        26.20        25.38        15.39        49.41         8.81 
TCGA-23-1030 TCGA-23-1032 TCGA-23-1109 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 
       29.13         2.24        51.35         3.22        31.20        68.68 
TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 TCGA-23-1122 TCGA-23-1123 
        4.57        33.30        86.01       129.96        39.09        33.47 
TCGA-23-2072 TCGA-23-2078 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-1104 
       24.95        87.48        11.64        21.80        41.56        63.55 
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-24-1428 TCGA-24-1431 TCGA-24-1436 
        6.02         5.95         5.36        17.39        19.17         8.55 
TCGA-24-1463 TCGA-24-1466 TCGA-24-1471 TCGA-24-1545 TCGA-24-1548 TCGA-24-1552 
       72.92        45.14         1.18        57.40        16.21        41.39 
TCGA-24-1555 TCGA-24-1558 TCGA-24-1560 TCGA-24-1564 TCGA-24-1567 TCGA-24-1842 
       88.50        19.53        44.09        25.87        17.23         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1850 TCGA-24-1923 
        3.48         3.72         4.37        11.28         5.52        22.68 
TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 TCGA-24-2020 TCGA-24-2023 
       30.21        16.44        11.05        81.11       152.02        44.84 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2260 TCGA-24-2262 TCGA-24-2267 TCGA-24-2280 
      109.71        14.43        36.16         0.36        47.54        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-25-1315 TCGA-25-1316 
       53.26         1.02        26.96        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1626 
        1.02        34.98        36.95         2.99        12.00        15.81 
TCGA-25-1627 TCGA-25-1631 TCGA-25-1635 TCGA-25-1870 TCGA-25-2391 TCGA-25-2392 
        0.36         0.30        51.22        14.96        49.05         1.02 
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-29-1688 TCGA-29-1693 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 
       26.99        78.90       101.79        31.20        68.32         0.53 
TCGA-29-1701 TCGA-29-1705 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1764 
       16.90        18.25        34.62        17.00        85.68        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 
       39.12        22.98        24.36        22.55        12.36        12.30 
TCGA-29-1781 TCGA-29-1783 TCGA-29-1785 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 
        8.38         7.23        34.62        65.00        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-30-1714 TCGA-30-1718 TCGA-30-1855 TCGA-30-1856 
       42.25        11.84        38.07        51.91         2.47        15.68 
TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 TCGA-30-1866 TCGA-30-1887 TCGA-31-1944 
        0.26        34.78         6.12        36.62        24.26        45.57 
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-36-1574 TCGA-36-1576 TCGA-36-2532 
       29.10        21.53        22.85        22.55        30.08        29.49 
TCGA-36-2543 TCGA-36-2545 TCGA-36-2548 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        2.24        18.31        14.17        42.02         7.46        40.77 
TCGA-42-2593 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-59-2348 TCGA-59-2350 
        1.48         1.74        29.00        25.08       180.20        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 TCGA-59-A5PD TCGA-61-1722 
      116.12         9.40         2.14         5.42        20.52         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         8.05 

$`DEL PEAK 27(16P13.3) WILD-TYPE`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1361 TCGA-04-1365 
       18.51        65.52        63.09        65.46        32.52        76.57 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1525 TCGA-04-1530 TCGA-04-1542 TCGA-04-1646 
       82.39        56.55        38.37       119.08        84.20        27.88 
TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 
       28.64        36.23        31.86        45.37        29.16         9.47 
TCGA-09-0366 TCGA-09-0369 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 
       57.76        35.57        38.43        89.33        74.93        41.62 
TCGA-09-1668 TCGA-09-1672 TCGA-09-1674 TCGA-09-1675 TCGA-09-2048 TCGA-09-2049 
       55.36         5.85         8.55        97.55         4.54       112.41 
TCGA-09-2051 TCGA-09-2056 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       63.09        12.46        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0936 TCGA-13-0714 
       33.24        32.28        11.70         3.91        35.80         6.21 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0726 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 
       39.58        12.39        31.10         2.50        11.54        34.06 
TCGA-13-0762 TCGA-13-0768 TCGA-13-0792 TCGA-13-0797 TCGA-13-0802 TCGA-13-0804 
       32.25         8.45        36.72         8.71         8.19        35.28 
TCGA-13-0888 TCGA-13-0890 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0908 
       70.39        67.99        57.47        57.07        19.36        44.84 
TCGA-13-0911 TCGA-13-0919 TCGA-13-0921 TCGA-13-1403 TCGA-13-1404 TCGA-13-1409 
       27.72        14.89         4.64        10.88         6.61         6.84 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1477 TCGA-13-1482 TCGA-13-1483 TCGA-13-1485 
        4.21         5.33        54.64        61.71        29.42        20.68 
TCGA-13-1487 TCGA-13-1496 TCGA-13-1499 TCGA-13-1504 TCGA-13-1505 TCGA-13-1510 
       22.39         4.24        38.40        16.57         4.21         2.56 
TCGA-13-1511 TCGA-13-2059 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FU TCGA-20-0987 
        3.91        12.23         8.61         6.28         8.42        23.05 
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-23-1026 TCGA-23-1027 TCGA-23-1031 
       47.54        42.54        40.54        26.83        31.76        18.90 
TCGA-23-1110 TCGA-23-1120 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 
       54.51         4.27         6.38        58.13         0.53       115.89 
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-24-0968 TCGA-24-0980 TCGA-24-0982 TCGA-24-1103 TCGA-24-1105 
        7.63        19.66         7.66        22.32        54.12        47.41 
TCGA-24-1413 TCGA-24-1427 TCGA-24-1430 TCGA-24-1434 TCGA-24-1435 TCGA-24-1464 
        6.31         4.83        28.37        18.67        43.53        12.46 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1474 TCGA-24-1544 TCGA-24-1546 
      105.99         9.11         3.45        22.22        26.96        64.27 
TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 
       56.58        41.06        51.91        58.09        70.62        39.88 
TCGA-24-1562 TCGA-24-1563 TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 
       45.50        47.70        10.26        90.15        88.37        48.33 
TCGA-24-1616 TCGA-24-1845 TCGA-24-1849 TCGA-24-1920 TCGA-24-2019 TCGA-24-2024 
       38.24         3.81         5.79         9.80         4.87        58.16 
TCGA-24-2026 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 TCGA-24-2038 
       34.82        53.95        18.48        28.18        64.01        44.52 
TCGA-24-2254 TCGA-24-2261 TCGA-24-2271 TCGA-24-2289 TCGA-25-1319 TCGA-25-1321 
       57.07         0.79        31.63        67.36        65.00        33.96 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1628 TCGA-25-1630 TCGA-25-1632 
        2.96        18.58        18.02        20.61         7.86        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       60.59        35.54        24.99        18.05        85.05        13.02 
TCGA-25-2393 TCGA-25-2396 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1694 
       38.04         3.02        31.00        44.71        47.18        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1702 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
        0.79        33.70        18.67        59.67        41.98        29.23 
TCGA-29-1763 TCGA-29-1768 TCGA-29-1774 TCGA-29-1776 TCGA-29-1778 TCGA-29-1784 
       66.81        31.23        17.33        11.84        14.93         5.36 
TCGA-29-2414 TCGA-29-2427 TCGA-29-2434 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1853 
       86.17        62.47        11.47         9.76        21.04        36.26 
TCGA-30-1859 TCGA-30-1860 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 
       48.10        44.91         1.22        57.57        30.05        48.79 
TCGA-31-1946 TCGA-31-1956 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       30.18        44.12         8.55        25.74        27.85        24.23 
TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.69        35.05        33.01        29.82        25.91        25.08 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2544 TCGA-36-2547 TCGA-36-2549 TCGA-36-2551 
       23.80        21.60        20.98        20.52         6.05        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2588 TCGA-57-1582 
       11.47         7.99        26.04        23.74         9.44        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1586 TCGA-57-1994 TCGA-59-2349 TCGA-59-2354 
       11.38        21.14        22.32        25.02        80.12        34.39 
TCGA-59-2372 TCGA-61-1721 TCGA-61-1727 TCGA-61-1728 TCGA-61-1733 TCGA-61-1738 
       44.81        11.11        18.54        27.88        31.79        35.80 
TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 TCGA-61-1901 TCGA-61-1911 TCGA-61-1915 
        2.43        43.69         5.79        11.41        42.51        67.76 
TCGA-61-1918 TCGA-61-2000 TCGA-61-2002 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       15.75        14.50        17.98        39.85        30.64         1.18 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 TCGA-61-2101 TCGA-61-2102 
       45.96        45.40        51.72        61.64        55.50         6.48 
TCGA-61-2104 TCGA-61-2110 TCGA-61-2111 TCGA-OY-A56Q 
       76.87        44.52       125.75        18.94 

  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                        180.20                         125.75 
  DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE 
                        26.565                         28.900 
[1] "0.3 - 180.2 (26.6)" "0.5 - 125.8 (28.9)"
[1] "hr=" "1"  
D60V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 27(16P13.3) MUTATED         2   299                1
  DEL PEAK 27(16P13.3) WILD-TYPE       0   258                1
D60V3, multiclass
                  clus
vv                 DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     299                            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"
D60V4, continuous
D60V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(16P13.3) MUTATED     1 307
  DEL PEAK 27(16P13.3) WILD-TYPE   2 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16P13.3) MUTATED      1  307
  DEL PEAK 27(16P13.3) WILD-TYPE    2  261
     clus
vv    DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE
  NO                             1                              2
  YES                          307                            261
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 27(16P13.3) MUTATED    7 12  3  1
  DEL PEAK 27(16P13.3) WILD-TYPE  7 14  2  2
D60V6, multiclass
    clus
vv   DEL PEAK 27(16P13.3) MUTATED DEL PEAK 27(16P13.3) WILD-TYPE
  R0                            7                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(16P13.3) MUTATED                                  2     9
  DEL PEAK 27(16P13.3) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(16P13.3) MUTATED                          16
  DEL PEAK 27(16P13.3) WILD-TYPE                        16
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(16P13.3) MUTATED                                           1
  DEL PEAK 27(16P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 27(16P13.3) MUTATED     262
  DEL PEAK 27(16P13.3) WILD-TYPE   213
D60V7, multiclass
                                           clus
vv                                          DEL PEAK 27(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              262
                                           clus
vv                                          DEL PEAK 27(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                  9
  BLACK OR AFRICAN AMERICAN                                             16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                213
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(16P13.3) MUTATED     4 179
  DEL PEAK 27(16P13.3) WILD-TYPE   6 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16P13.3) MUTATED      4  179
  DEL PEAK 27(16P13.3) WILD-TYPE    6  146
                        clus
vv                       DEL PEAK 27(16P13.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          179
                        clus
vv                       DEL PEAK 27(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            146
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 28(16Q22.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(16Q22.1) MUTATED   214 230
  DEL PEAK 28(16Q22.1) WILD-TYPE  52  60
  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                           444                            112 
  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                           230                             60 
$`DEL PEAK 28(16Q22.1) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1342 
       40.24        41.00         1.81        49.15         2.01        18.51 
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-04-1356 TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 
       65.46        49.28        32.52        44.32        33.67        76.57 
TCGA-04-1367 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 
       71.47        41.59        19.99        38.37       119.08        55.43 
TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        64.64        36.23        31.86        47.70        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1661 TCGA-09-1662 TCGA-09-1666 TCGA-09-1667 
       57.76        17.98        38.43        89.33        57.60        61.87 
TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 
       55.36        30.51        17.98         8.55        97.55         6.18 
TCGA-09-2044 TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 
        6.12         4.54       112.41        71.11        63.09        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 
       20.94        26.93        54.31        25.91        81.47        18.51 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 
       33.24        32.28        35.44        35.80        15.12        19.86 
TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 
        6.21        24.59        44.55        39.58         2.73        31.10 
TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       15.19        17.82        55.17         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0792 TCGA-13-0793 
       11.54        34.06        32.25        31.04        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 
       30.35        19.59         8.71         8.28         8.19        35.28 
TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 
       35.28        13.61        68.94       107.18        91.40        74.27 
TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       66.67        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        56.15        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       21.17        14.89        13.81         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 
        6.61         7.36         6.05         5.92         4.70         4.21 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 
        5.33        87.06        29.42        98.04        22.39        70.82 
TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       82.88        52.44        73.55        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
       54.31        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 
        4.21         4.41         4.77         4.18         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-A5FT 
       14.24        12.23         8.61        10.78         8.75        54.77 
TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        8.42        23.05        25.94        26.20        27.52        25.38 
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        42.54        40.54 
TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       26.83        31.76        49.41         8.81        29.13        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         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
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-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        11.64 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       41.56        22.32        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 TCGA-24-1425 
        6.38         7.82         7.99         7.86         0.76         5.95 
TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1434 
        5.36         4.83        17.39        28.37        19.17        18.67 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1466 TCGA-24-1469 
       43.53         8.55        72.92        12.46        45.14         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-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 
       41.06        51.91        41.39        88.50        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-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1845 TCGA-24-1846 
       90.15         8.32         3.48         3.72         3.81         4.37 
TCGA-24-1847 TCGA-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
       11.28         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-24-2026 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       34.82        14.43        53.95        18.48        28.18        64.01 
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-24-2281 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-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 
        1.02        26.96        32.02        51.06        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 
       34.98        65.00        36.95         2.99        12.00         2.96 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 
       15.81         0.36        20.61         7.86         0.30        56.94 
TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 
       60.59        51.22        14.96        24.99        18.05        85.05 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2398 
       13.02        49.05         1.02        38.04         3.02        45.01 
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        47.18 
TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 
      101.79        38.53         0.79        33.70        31.20        68.32 
TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1761 
        0.53        16.90        18.67        59.67        18.25        17.00 
TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       85.68        66.81        62.93        31.23        22.98        24.36 
TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 TCGA-29-1784 
       22.55        12.36        12.30         8.38         7.23         5.36 
TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
       34.62        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 
       42.25        11.84        11.47        21.04        38.07        36.26 
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-30-1867 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-31-1959 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-36-1577 
       29.10        21.53        22.85         8.55        30.08        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 TCGA-36-2537 
       27.85        24.23        35.05        33.01        29.82        25.91 
TCGA-36-2542 TCGA-36-2543 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 TCGA-36-2551 
       21.60         2.24        18.31        20.52        14.17        16.18 
TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 
       11.47        23.74         9.44        42.02         7.46         1.48 
TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 
       24.03        21.14         1.74        22.32        29.00        25.08 
TCGA-57-1994 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2355 TCGA-59-2363 
       25.02        22.32       116.12         9.40         2.14         5.42 
TCGA-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
       20.52         8.09        20.94        31.43        18.54        27.88 
TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1738 TCGA-61-1740 
        4.34        31.79        48.79        44.84        35.80         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 
       33.67        43.69         1.45         8.42         5.79        11.41 
TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 
        9.07        34.13        31.30        37.05        48.92        56.61 
TCGA-61-1917 TCGA-61-1919 TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 
       43.43        38.17         2.01         5.52        14.50         4.01 
TCGA-61-2008 TCGA-61-2012 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 
       30.64        30.64         4.80         4.77        71.74        60.62 
TCGA-61-2098 TCGA-61-2102 TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 
       65.52         6.48        76.87        20.68       125.75        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         8.05 

$`DEL PEAK 28(16Q22.1) WILD-TYPE`
TCGA-04-1338 TCGA-04-1371 TCGA-04-1514 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 
       46.62        82.39        56.55        29.10        84.20        27.88 
TCGA-04-1648 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1659 TCGA-09-1664 
       28.64        29.16         9.47        35.57         9.99        74.93 
TCGA-09-1665 TCGA-09-1672 TCGA-09-1673 TCGA-09-2045 TCGA-09-2056 TCGA-10-0933 
       41.62         5.85         3.02        35.15        12.46        11.70 
TCGA-10-0934 TCGA-13-0725 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0799 
        3.91        12.39        21.40         8.45        38.93         7.79 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0901 TCGA-13-0921 TCGA-13-1409 TCGA-13-1477 
        8.12        43.86        19.36         4.64         6.84        54.64 
TCGA-13-1482 TCGA-13-1485 TCGA-13-1510 TCGA-13-2071 TCGA-20-0996 TCGA-20-1684 
       61.71        20.68         2.56         6.28        72.20        19.10 
TCGA-23-1024 TCGA-23-1032 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 TCGA-24-0975 
       15.39         2.24        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        18.02        35.54        12.00        31.00        78.90 
TCGA-29-1690 TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1766 TCGA-29-1774 
       44.71        41.98        29.23        34.62        39.12        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-3P-A9WA TCGA-42-2582 TCGA-42-2591 
       23.80        20.98         6.05         7.99        26.04        40.77 
TCGA-57-1583 TCGA-59-2348 TCGA-59-2349 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 
       11.38       180.20        80.12        34.39        44.81        11.11 
TCGA-61-1734 TCGA-61-1903 TCGA-61-1911 TCGA-61-1915 TCGA-61-1918 TCGA-61-2002 
       28.47        13.02        42.51        67.76        15.75        17.98 
TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 
       39.85         1.18        45.96        45.40        51.72        61.64 
TCGA-61-2096 TCGA-61-2101 TCGA-61-2110 TCGA-OY-A56Q 
       58.39        55.50        44.52        18.94 

  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                        152.02                         180.20 
  DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE 
                        26.975                         29.360 
[1] "0.3 - 152.0 (27.0)" "0.5 - 180.2 (29.4)"
[1] "hr=" "1.1"
D61V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 28(16Q22.1) MUTATED         1   444                1
  DEL PEAK 28(16Q22.1) WILD-TYPE       1   113                1
D61V3, multiclass
                  clus
vv                 DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     444                            113
  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"
D61V4, continuous
D61V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(16Q22.1) MUTATED     3 453
  DEL PEAK 28(16Q22.1) WILD-TYPE   0 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16Q22.1) MUTATED      3  453
  DEL PEAK 28(16Q22.1) WILD-TYPE    0  115
     clus
vv    DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE
  NO                             3                              0
  YES                          453                            115
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 28(16Q22.1) MUTATED    9 23  5  1
  DEL PEAK 28(16Q22.1) WILD-TYPE  5  3  0  2
D61V6, multiclass
    clus
vv   DEL PEAK 28(16Q22.1) MUTATED DEL PEAK 28(16Q22.1) WILD-TYPE
  R0                            9                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(16Q22.1) MUTATED                                  3    14
  DEL PEAK 28(16Q22.1) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(16Q22.1) MUTATED                          25
  DEL PEAK 28(16Q22.1) WILD-TYPE                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(16Q22.1) MUTATED                                           1
  DEL PEAK 28(16Q22.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 28(16Q22.1) MUTATED     379
  DEL PEAK 28(16Q22.1) WILD-TYPE    96
D61V7, multiclass
                                           clus
vv                                          DEL PEAK 28(16Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              379
                                           clus
vv                                          DEL PEAK 28(16Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       0
  ASIAN                                                                  4
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 96
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(16Q22.1) MUTATED     7 261
  DEL PEAK 28(16Q22.1) WILD-TYPE   3  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16Q22.1) MUTATED      7  261
  DEL PEAK 28(16Q22.1) WILD-TYPE    3   64
                        clus
vv                       DEL PEAK 28(16Q22.1) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          261
                        clus
vv                       DEL PEAK 28(16Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             64
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 29(16Q23.1) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(16Q23.1) MUTATED   204 232
  DEL PEAK 29(16Q23.1) WILD-TYPE  62  58
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           436                            120 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           232                             58 
$`DEL PEAK 29(16Q23.1) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
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-04-1356 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        71.47 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1638 
       82.39        41.59        19.99        38.37       119.08        55.43 
TCGA-04-1644 TCGA-04-1649 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        64.64        36.23        31.86        47.70        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1665 
       57.76        17.98         9.99        38.43        89.33        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1673 
       57.60        61.87        55.36        30.51        17.98         3.02 
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-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-10-0925 TCGA-10-0926 TCGA-10-0927 
       63.09        39.75        20.94        54.31        25.91        81.47 
TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 
       18.51        33.24        32.28        35.44        35.80        15.12 
TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 
       19.86         6.21        24.59        44.55        39.58         2.73 
TCGA-13-0726 TCGA-13-0727 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 
       31.10        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        34.06        32.25        31.04        21.40 
TCGA-13-0791 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0801 
       38.93        28.70        30.35        19.59         8.71         8.28 
TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
        8.19        35.28        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0906 
       43.36        57.47        56.15        57.07        47.38        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0916 TCGA-13-0919 
       44.84        37.08        27.72        34.06        21.17        14.89 
TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 
       13.81         6.41         6.08        10.88         6.61         7.36 
TCGA-13-1407 TCGA-13-1408 TCGA-13-1410 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 
        6.05         5.92         4.70         4.21         5.33        87.06 
TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 
       29.42        98.04        22.39        70.82        82.88        52.44 
TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 
       73.55        38.20        49.25         4.24        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        13.97        16.57         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 
        4.18         3.91         3.09        14.24         8.61        10.78 
TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 TCGA-20-1682 
        8.75        54.77         8.42        23.05        26.20        27.52 
TCGA-20-1683 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1023 
       25.38        16.70         2.93         2.66        42.54        40.54 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1032 
       31.76        49.41         8.81        29.13        18.90         2.24 
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         4.57        33.30 
TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 
       86.01       129.96         4.27         6.38        39.09        33.47 
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-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        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        19.17 
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        53.95 
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 
       51.06        37.02         1.02        34.98        65.00        36.95 
TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1627 
        2.99        12.00         2.96        18.58        15.81         0.36 
TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1635 TCGA-25-1870 
       20.61         0.30        56.94        60.59        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       24.99        18.05        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        47.18       101.79        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
        0.79        33.70        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1710 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.67        59.67        29.23        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 
       62.93        39.12        31.23        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        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        45.11         4.90        42.25        11.84 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 TCGA-30-1860 
       21.04        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         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1584 TCGA-57-1585 
        7.46        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-59-A5PD TCGA-61-1722 TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 
        5.42        20.52         8.09        20.94        31.43        18.54 
TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 
       27.88         4.34        31.79        48.79        44.84         2.43 
TCGA-61-1741 TCGA-61-1743 TCGA-61-1895 TCGA-61-1899 TCGA-61-1900 TCGA-61-1904 
       33.67        43.69         1.45         8.42         5.79         9.07 
TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 
       34.13        31.30        37.05        48.92        56.61        38.17 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2000 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        2.01         5.52        14.50         4.01        30.64        30.64 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2097 TCGA-61-2098 TCGA-61-2102 
        4.80         4.77        71.74        60.62        65.52         6.48 
TCGA-61-2104 TCGA-61-2109 TCGA-61-2111 TCGA-61-2113 TCGA-61-2612 TCGA-61-2613 
       76.87        20.68       125.75        22.22         6.35        31.07 
TCGA-61-2614 TCGA-OY-A56P TCGA-VG-A8LO TCGA-WR-A838 
        8.61        39.68         0.79         8.05 

$`DEL PEAK 29(16Q23.1) WILD-TYPE`
TCGA-04-1335 TCGA-04-1351 TCGA-04-1514 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 
        1.81        65.46        56.55        29.10        84.20        27.88 
TCGA-04-1648 TCGA-09-0364 TCGA-09-0365 TCGA-09-0369 TCGA-09-1664 TCGA-09-1672 
       28.64        29.16         9.47        35.57        74.93         5.85 
TCGA-09-2045 TCGA-09-2050 TCGA-09-2055 TCGA-09-2056 TCGA-10-0933 TCGA-10-0934 
       35.15        71.11        26.93        12.46        11.70         3.91 
TCGA-13-0725 TCGA-13-0768 TCGA-13-0792 TCGA-13-0799 TCGA-13-0800 TCGA-13-0803 
       12.39         8.45        36.72         7.79         8.12        43.86 
TCGA-13-0891 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0913 TCGA-13-0921 
       69.01        19.36        48.33        47.84        29.98         4.64 
TCGA-13-1409 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 TCGA-13-1501 TCGA-13-1510 
        6.84        54.64        61.71        20.68        32.84         2.56 
TCGA-13-2059 TCGA-13-2071 TCGA-20-0990 TCGA-20-0996 TCGA-20-1684 TCGA-23-1021 
       12.23         6.28        25.94        72.20        19.10        47.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1110 TCGA-23-1124 TCGA-23-1809 TCGA-24-0980 
       15.39        26.83        54.51        58.13         0.53         7.66 
TCGA-24-1423 TCGA-24-1424 TCGA-24-1467 TCGA-24-1546 TCGA-24-1549 TCGA-24-1553 
        6.25         6.02       105.99        64.27        56.58        58.09 
TCGA-24-1562 TCGA-24-1604 TCGA-24-1616 TCGA-24-1924 TCGA-24-2036 TCGA-24-2038 
       45.50        88.37        38.24        30.21        64.01        44.52 
TCGA-24-2290 TCGA-25-1314 TCGA-25-1321 TCGA-25-1625 TCGA-25-1630 TCGA-25-1634 
       36.23        32.02        33.96        18.02         7.86        35.54 
TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 
       31.00        78.90        44.71        18.25        41.98        34.62 
TCGA-29-1770 TCGA-29-1774 TCGA-29-1778 TCGA-29-2427 TCGA-29-2434 TCGA-29-2436 
       24.36        17.33        14.93        62.47        11.47         9.76 
TCGA-30-1718 TCGA-30-1855 TCGA-30-1859 TCGA-30-1862 TCGA-36-1574 TCGA-36-1581 
       51.91         2.47        48.10         6.12        22.55        24.69 
TCGA-36-2532 TCGA-36-2537 TCGA-36-2538 TCGA-36-2540 TCGA-36-2544 TCGA-36-2545 
       29.49        25.91        25.08        23.80        20.98        18.31 
TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-57-1583 TCGA-57-1586 TCGA-59-2348 
        6.05         7.99        26.04        11.38        22.32       180.20 
TCGA-59-2349 TCGA-59-2351 TCGA-59-2354 TCGA-59-2372 TCGA-61-1721 TCGA-61-1734 
       80.12       116.12        34.39        44.81        11.11        28.47 
TCGA-61-1738 TCGA-61-1901 TCGA-61-1903 TCGA-61-1911 TCGA-61-1915 TCGA-61-1917 
       35.80        11.41        13.02        42.51        67.76        43.43 
TCGA-61-1918 TCGA-61-2002 TCGA-61-2009 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       15.75        17.98        39.85         1.18        45.96        45.40 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2096 TCGA-61-2101 TCGA-61-2110 TCGA-OY-A56Q 
       51.72        61.64        58.39        55.50        44.52        18.94 

  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                        152.02                         180.20 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                        27.255                         29.325 
[1] "0.3 - 152.0 (27.3)" "0.5 - 180.2 (29.3)"
[1] "hr=" "1.2"
D62V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 29(16Q23.1) MUTATED         1   435                2
  DEL PEAK 29(16Q23.1) WILD-TYPE       1   122                0
D62V3, multiclass
                  clus
vv                 DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     435                            122
  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"
D62V4, continuous
D62V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.1) MUTATED     3 443
  DEL PEAK 29(16Q23.1) WILD-TYPE   0 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED      3  443
  DEL PEAK 29(16Q23.1) WILD-TYPE    0  125
     clus
vv    DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  NO                             3                              0
  YES                          443                            125
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 29(16Q23.1) MUTATED    7 21  5  1
  DEL PEAK 29(16Q23.1) WILD-TYPE  7  5  0  2
D62V6, multiclass
    clus
vv   DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  R0                            7                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(16Q23.1) MUTATED                                  3    14
  DEL PEAK 29(16Q23.1) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(16Q23.1) MUTATED                          25
  DEL PEAK 29(16Q23.1) WILD-TYPE                         7
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 29(16Q23.1) MUTATED                                           1
  DEL PEAK 29(16Q23.1) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 29(16Q23.1) MUTATED     373
  DEL PEAK 29(16Q23.1) WILD-TYPE   102
D62V7, multiclass
                                           clus
vv                                          DEL PEAK 29(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               14
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              373
                                           clus
vv                                          DEL PEAK 29(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       0
  ASIAN                                                                  4
  BLACK OR AFRICAN AMERICAN                                              7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                102
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.1) MUTATED     6 252
  DEL PEAK 29(16Q23.1) WILD-TYPE   4  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED      6  252
  DEL PEAK 29(16Q23.1) WILD-TYPE    4   73
                        clus
vv                       DEL PEAK 29(16Q23.1) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          252
                        clus
vv                       DEL PEAK 29(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             73
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 30(17P12) MUTATION ANALYSIS
D63V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 30(17P12) MUTATED   219 253
  DEL PEAK 30(17P12) WILD-TYPE  47  37
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         472                           84 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                         253                           37 
$`DEL PEAK 30(17P12) MUTATED`
TCGA-04-1331 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1343 
       40.24         1.81        49.15         2.01        46.62        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-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       44.32        33.67        76.57        71.47        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       19.99        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-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 
       47.70        45.37        29.16         9.47        57.76        17.98 
TCGA-09-0369 TCGA-09-1659 TCGA-09-1662 TCGA-09-1664 TCGA-09-1665 TCGA-09-1666 
       35.57         9.99        89.33        74.93        41.62        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-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 
       97.55         6.12        35.15       112.41        71.11        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 TCGA-10-0927 TCGA-10-0930 
       20.94        26.93        12.46        25.91        81.47        33.24 
TCGA-10-0933 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 
       11.70        35.80        15.12        19.86         6.21        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        31.10        15.19 
TCGA-13-0730 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0760 TCGA-13-0761 
       17.82         2.50        11.18        11.38        11.54        34.06 
TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 
       31.04        21.40         8.45        38.93        36.72        28.70 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 
       30.35        19.59         8.71         7.79         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
       91.40        74.27        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 
       69.01        43.36        57.47        57.07        19.36        47.38 
TCGA-13-0904 TCGA-13-0905 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       48.33        47.84        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 
       10.88         6.61         7.36         6.05         5.92         6.84 
TCGA-13-1410 TCGA-13-1411 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.70         4.21        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
       32.84        16.57         4.18         2.56         3.91         3.09 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 
       10.78         8.75         6.28        54.77         8.42        23.05 
TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1687 
       25.94        26.20        27.52        19.10        16.70         2.66 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 
       47.54        40.54        15.39        26.83        31.76        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         2.24        51.35        54.51 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1119 
        3.22        31.20         4.57        33.30        86.01       129.96 
TCGA-23-1120 TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2072 
        4.27         6.38        39.09        33.47        58.13        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-24-0968 TCGA-24-0970 TCGA-24-0975 
        4.70         4.50         7.63        19.66        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 
       19.17        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        53.95        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        32.02        37.02         1.02 
TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 
       34.98        65.00        36.95        33.96         2.99        12.00 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 
        2.96        18.02         0.36        20.61         7.86         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       56.94        60.59        35.54        51.22        14.96        24.99 
TCGA-25-1877 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       18.05        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 
       47.18       101.79        38.53         0.79        33.70        31.20 
TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 
       68.32         0.53        16.90        18.67        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        17.00        85.68        62.93        31.23 
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        34.62        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        11.84        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-3P-A9WA TCGA-42-2582 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 
        6.05         7.99        26.04        23.74        42.02         7.46 
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-57-1993 TCGA-59-2348 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 
       25.08       180.20        22.32       116.12         9.40        34.39 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 
        2.14         5.42        44.81        20.52        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-61-1901 TCGA-61-1903 TCGA-61-1906 TCGA-61-1907 TCGA-61-1913 
        8.42        11.41        13.02        34.13        31.30        48.92 
TCGA-61-1914 TCGA-61-1915 TCGA-61-1917 TCGA-61-1918 TCGA-61-1919 TCGA-61-1995 
       56.61        67.76        43.43        15.75        38.17         2.01 
TCGA-61-1998 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2012 
        5.52        14.50        17.98         4.01        30.64        30.64 
TCGA-61-2016 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 TCGA-61-2095 TCGA-61-2096 
        1.18        45.40         4.77        71.74        61.64        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-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

$`DEL PEAK 30(17P12) WILD-TYPE`
TCGA-04-1332 TCGA-04-1342 TCGA-04-1356 TCGA-04-1361 TCGA-04-1516 TCGA-09-1661 
       41.00        18.51        49.28        32.52        41.59        38.43 
TCGA-09-1674 TCGA-09-2043 TCGA-09-2048 TCGA-09-2051 TCGA-10-0925 TCGA-10-0928 
        8.55         6.18         4.54        63.09        54.31        18.51 
TCGA-10-0931 TCGA-10-0934 TCGA-10-0935 TCGA-13-0751 TCGA-13-0762 TCGA-13-0800 
       32.28         3.91        35.44        55.17        32.25         8.12 
TCGA-13-0899 TCGA-13-0906 TCGA-13-0920 TCGA-13-1412 TCGA-13-1477 TCGA-13-1485 
       56.15        44.94        13.81         5.33        54.64        20.68 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.21         4.41         4.77        14.24        12.23         8.61 
TCGA-20-0996 TCGA-20-1683 TCGA-20-1686 TCGA-23-1022 TCGA-23-1114 TCGA-23-1809 
       72.20        25.38         2.93        42.54        68.68         0.53 
TCGA-24-1428 TCGA-24-1474 TCGA-24-1556 TCGA-24-1565 TCGA-24-1924 TCGA-24-2035 
       17.39        22.22        70.62        10.26        30.21        28.18 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2262 TCGA-24-2289 TCGA-25-1315 TCGA-25-1623 
       44.52        57.07         0.36        67.36        51.06        18.58 
TCGA-25-1626 TCGA-25-1878 TCGA-25-2397 TCGA-25-2398 TCGA-25-2408 TCGA-29-1690 
       15.81        85.05        12.00        45.01        31.00        44.71 
TCGA-29-1710 TCGA-29-1763 TCGA-29-1766 TCGA-29-1774 TCGA-29-2429 TCGA-29-2434 
       29.23        66.81        39.12        17.33         4.90        11.47 
TCGA-29-2436 TCGA-29-A5NZ TCGA-36-1569 TCGA-36-1578 TCGA-36-1581 TCGA-36-2540 
        9.76        21.04        29.10        27.85        24.69        23.80 
TCGA-36-2542 TCGA-36-2551 TCGA-36-2552 TCGA-42-2588 TCGA-57-1586 TCGA-57-1992 
       21.60        16.18        11.47         9.44        22.32        29.00 
TCGA-57-1994 TCGA-59-2349 TCGA-61-1721 TCGA-61-1722 TCGA-61-1900 TCGA-61-1904 
       25.02        80.12        11.11         8.09         5.79         9.07 
TCGA-61-1910 TCGA-61-1911 TCGA-61-2009 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 
       37.05        42.51        39.85        45.96         4.80        51.72 

  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                        0.26                         0.36 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                      180.20                        85.05 
  DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE 
                      28.670                       24.855 
[1] "0.3 - 180.2 (28.7)" "0.4 - 85.0 (24.9)" 
[1] "hr=" "1"  
D63V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 30(17P12) MUTATED         2   473                1
  DEL PEAK 30(17P12) WILD-TYPE       0    84                1
D63V3, multiclass
                  clus
vv                 DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  OMENTUM                                   2                            0
  OVARY                                   473                           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"
D63V4, continuous
D63V5, binary
                              cls
clus                             0   1
  DEL PEAK 30(17P12) MUTATED     3 482
  DEL PEAK 30(17P12) WILD-TYPE   0  86
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(17P12) MUTATED      3  482
  DEL PEAK 30(17P12) WILD-TYPE    0   86
     clus
vv    DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  NO                           3                            0
  YES                        482                           86
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 30(17P12) MUTATED   10 22  4  3
  DEL PEAK 30(17P12) WILD-TYPE  4  4  1  0
D63V6, multiclass
    clus
vv   DEL PEAK 30(17P12) MUTATED DEL PEAK 30(17P12) WILD-TYPE
  R0                         10                            4
  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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(17P12) MUTATED                                  3    16
  DEL PEAK 30(17P12) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(17P12) MUTATED                          29
  DEL PEAK 30(17P12) WILD-TYPE                         3
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 30(17P12) MUTATED                                           1   400
  DEL PEAK 30(17P12) WILD-TYPE                                         0    75
D63V7, multiclass
                                           clus
vv                                          DEL PEAK 30(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   3
  ASIAN                                                             16
  BLACK OR AFRICAN AMERICAN                                         29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            400
                                           clus
vv                                          DEL PEAK 30(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               75
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                              cls
clus                             0   1
  DEL PEAK 30(17P12) MUTATED     8 276
  DEL PEAK 30(17P12) WILD-TYPE   2  49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(17P12) MUTATED      8  276
  DEL PEAK 30(17P12) WILD-TYPE    2   49
                        clus
vv                       DEL PEAK 30(17P12) MUTATED
  HISPANIC OR LATINO                              8
  NOT HISPANIC OR LATINO                        276
                        clus
vv                       DEL PEAK 30(17P12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           49
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 31(17Q11.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(17Q11.2) MUTATED   216 237
  DEL PEAK 31(17Q11.2) WILD-TYPE  50  53
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                           453                            103 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                           237                             53 
$`DEL PEAK 31(17Q11.2) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 
       40.24        41.00         1.81        49.15         2.01        46.62 
TCGA-04-1343 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        63.09        48.76        21.57        63.98        65.46 
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        71.47 
TCGA-04-1371 TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 
       82.39        56.55        19.99        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-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1664 TCGA-09-1667 TCGA-09-1668 
       17.98        35.57         9.99        74.93        61.87        55.36 
TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 TCGA-09-1673 TCGA-09-2044 TCGA-09-2049 
       30.51        17.98         5.85         3.02         6.12       112.41 
TCGA-09-2050 TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-10-0926 
       71.11        63.09        39.75        20.94        26.93        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-10-0938 
       81.47        18.51        33.24        32.28        15.12        19.86 
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-13-0757 TCGA-13-0758 
       31.10        15.19        17.82        55.17        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 
       11.54        34.06        32.25        21.40         8.45        38.93 
TCGA-13-0792 TCGA-13-0793 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 
       36.72        28.70        19.59         8.71         7.79         8.28 
TCGA-13-0802 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0883 TCGA-13-0884 
        8.19        43.86        35.28        35.28        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 
       43.36        57.47        57.07        19.36        47.38        48.33 
TCGA-13-0905 TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 
       47.84        44.94        44.84        37.08        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       29.98        21.17        14.89         4.64         6.41         6.08 
TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1409 TCGA-13-1410 
       10.88         6.61         7.36         6.05         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 
        4.21         5.33        87.06        61.71        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 
       22.39        70.82        82.88        52.44        73.55        38.20 
TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 
       49.25         4.24        54.31        37.61        38.40        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 
       32.84        16.57         4.21         4.41         4.77         4.18 
TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 
        2.56         3.91         3.09        12.23        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
        6.28         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        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 
       40.54        15.39        26.83        31.76        49.41         8.81 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 
       18.90         2.24        51.35        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         4.57        86.01       129.96         4.27        39.09 
TCGA-23-1123 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2081 TCGA-23-2084 
       33.47        24.95       115.89        87.48        77.00        49.84 
TCGA-23-2641 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0968 TCGA-24-0970 
        2.76         4.70         4.50         7.63        19.66        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-24-1105 TCGA-24-1413 TCGA-24-1416 TCGA-24-1418 TCGA-24-1419 TCGA-24-1422 
       47.41         6.31         6.38         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-24-1463 
       28.37        19.17        18.67        43.53         8.55        72.92 
TCGA-24-1464 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 
       12.46        45.14       105.99         9.11         3.45         1.18 
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-24-1567 TCGA-24-1603 
       44.09        45.50        47.70        25.87        17.23        90.15 
TCGA-24-1604 TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1845 
       88.37        48.33        38.24         8.32         3.48         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-24-1930 TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 
       16.44        11.05        81.11         4.87       152.02        58.16 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 
      109.71        14.43        53.95        18.48        64.01        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-24-2289 TCGA-24-2290 TCGA-24-2293 TCGA-24-2297 TCGA-24-2298 TCGA-25-1312 
       67.36        36.23        16.64        55.86        53.26         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 
       26.96        32.02        51.06        37.02         1.02        34.98 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 
       36.95        33.96         2.99        12.00         2.96        18.02 
TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 
        0.36        20.61         7.86         0.30        56.94        60.59 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2042 TCGA-25-2391 TCGA-25-2393 
       51.22        14.96        24.99        13.02        49.05        38.04 
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-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 TCGA-29-1696 
       26.99        78.90       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20        68.32         0.53        59.67        18.25        41.98 
TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       34.62        17.00        85.68        66.81        62.93        31.23 
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-29-2425 
       14.93         8.38         7.23         5.36        34.62        65.00 
TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
       62.47        45.11         4.90        42.25        11.84        11.47 
TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1856 TCGA-30-1857 TCGA-30-1859 
       38.07        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-31-1953 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1568 TCGA-36-1570 
        6.71        42.51        44.12         2.20        28.77        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-36-2530 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-36-2543 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-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 
        7.99        26.04         9.44        42.02         7.46        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-59-A5PD TCGA-61-1724 
        9.40        34.39         5.42        44.81        20.52        20.94 
TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       31.43        18.54        27.88         4.34        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-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 TCGA-61-1906 
        1.45         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-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 
        4.01        30.64        30.64         1.18        45.40         4.80 
TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2101 TCGA-61-2102 
        4.77        71.74        58.39        60.62        55.50         6.48 
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-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       18.94         0.79         8.05 

$`DEL PEAK 31(17Q11.2) WILD-TYPE`
TCGA-04-1342 TCGA-04-1346 TCGA-04-1516 TCGA-04-1644 TCGA-09-1661 TCGA-09-1662 
       18.51        65.52        41.59        48.89        38.43        89.33 
TCGA-09-1665 TCGA-09-1666 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2045 
       41.62        57.60         8.55        97.55         6.18        35.15 
TCGA-09-2048 TCGA-09-2056 TCGA-10-0925 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
        4.54        12.46        54.31        11.70         3.91        35.44 
TCGA-10-0936 TCGA-13-0755 TCGA-13-0764 TCGA-13-0794 TCGA-13-0800 TCGA-13-0807 
       35.80         2.50        31.04        30.35         8.12        13.61 
TCGA-13-0888 TCGA-13-0899 TCGA-13-0920 TCGA-13-1408 TCGA-13-1477 TCGA-13-1485 
       70.39        56.15        13.81         5.92        54.64        20.68 
TCGA-13-2057 TCGA-13-2060 TCGA-13-A5FT TCGA-20-0987 TCGA-20-0996 TCGA-23-1030 
       14.24         8.61        54.77        23.05        72.20        29.13 
TCGA-23-1117 TCGA-23-1121 TCGA-23-1124 TCGA-23-1809 TCGA-23-2079 TCGA-24-1417 
       33.30         6.38        58.13         0.53        91.66         7.82 
TCGA-24-1474 TCGA-24-1556 TCGA-24-1565 TCGA-24-1844 TCGA-24-1850 TCGA-24-2023 
       22.22        70.62        10.26         3.72         5.52        44.84 
TCGA-24-2026 TCGA-24-2035 TCGA-24-2038 TCGA-24-2260 TCGA-24-2261 TCGA-24-2295 
       34.82        28.18        44.52        36.16         0.79        33.11 
TCGA-25-1319 TCGA-25-1623 TCGA-25-1626 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 
       65.00        18.58        15.81        35.54        18.05        85.05 
TCGA-25-2392 TCGA-25-2396 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1701 
        1.02         3.02        31.00        44.71        47.18        16.90 
TCGA-29-1702 TCGA-29-1710 TCGA-29-1766 TCGA-29-1774 TCGA-29-2414 TCGA-29-2436 
       18.67        29.23        39.12        17.33        86.17         9.76 
TCGA-29-A5NZ TCGA-30-1718 TCGA-31-1951 TCGA-36-1569 TCGA-36-1581 TCGA-36-2529 
       21.04        51.91        22.49        29.10        24.69        35.05 
TCGA-36-2540 TCGA-36-2542 TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2593 
       23.80        21.60        16.18        11.47        23.74         1.48 
TCGA-57-1582 TCGA-57-1586 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2349 
       24.03        22.32        29.00        25.08        25.02        80.12 
TCGA-59-2355 TCGA-61-1721 TCGA-61-1722 TCGA-61-1904 TCGA-61-1911 TCGA-61-2009 
        2.14        11.11         8.09         9.07        42.51        39.85 
TCGA-61-2017 TCGA-61-2092 TCGA-61-2095 TCGA-61-2098 TCGA-61-2612 TCGA-61-2614 
       45.96        51.72        61.64        65.52         6.35         8.61 
TCGA-OY-A56P 
       39.68 

  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                          0.26                           0.53 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                        180.20                          97.55 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                         28.37                          25.08 
[1] "0.3 - 180.2 (28.4)" "0.5 - 97.5 (25.1)" 
[1] "hr=" "1"  
D64V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 31(17Q11.2) MUTATED         2   454                0
  DEL PEAK 31(17Q11.2) WILD-TYPE       0   103                2
D64V3, multiclass
                  clus
vv                 DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     454                            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"
D64V4, continuous
D64V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(17Q11.2) MUTATED     3 463
  DEL PEAK 31(17Q11.2) WILD-TYPE   0 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17Q11.2) MUTATED      3  463
  DEL PEAK 31(17Q11.2) WILD-TYPE    0  105
     clus
vv    DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE
  NO                             3                              0
  YES                          463                            105
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 31(17Q11.2) MUTATED   10 16  3  2
  DEL PEAK 31(17Q11.2) WILD-TYPE  4 10  2  1
D64V6, multiclass
    clus
vv   DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE
  R0                           10                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(17Q11.2) MUTATED                                  2    16
  DEL PEAK 31(17Q11.2) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(17Q11.2) MUTATED                          28
  DEL PEAK 31(17Q11.2) WILD-TYPE                         4
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(17Q11.2) MUTATED                                           1
  DEL PEAK 31(17Q11.2) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 31(17Q11.2) MUTATED     386
  DEL PEAK 31(17Q11.2) WILD-TYPE    89
D64V7, multiclass
                                           clus
vv                                          DEL PEAK 31(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                           28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              386
                                           clus
vv                                          DEL PEAK 31(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                  2
  BLACK OR AFRICAN AMERICAN                                              4
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 89
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(17Q11.2) MUTATED     9 266
  DEL PEAK 31(17Q11.2) WILD-TYPE   1  59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17Q11.2) MUTATED      9  266
  DEL PEAK 31(17Q11.2) WILD-TYPE    1   59
                        clus
vv                       DEL PEAK 31(17Q11.2) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          266
                        clus
vv                       DEL PEAK 31(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             59
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 32(18Q23) MUTATION ANALYSIS
D65V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 32(18Q23) MUTATED   181 185
  DEL PEAK 32(18Q23) WILD-TYPE  85 105
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         366                          190 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                         185                          105 
$`DEL PEAK 32(18Q23) MUTATED`
TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1343 TCGA-04-1346 
       41.00         1.81        49.15        46.62        11.87        65.52 
TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       63.09        48.76        21.57        63.98        65.46        49.28 
TCGA-04-1361 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1516 TCGA-04-1517 
       32.52        44.32        33.67        76.57        41.59        19.99 
TCGA-04-1530 TCGA-04-1644 TCGA-04-1646 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 
      119.08        48.89        27.88        36.23        31.86        47.70 
TCGA-04-1655 TCGA-09-0367 TCGA-09-1665 TCGA-09-1666 TCGA-09-1667 TCGA-09-1669 
       45.37        17.98        41.62        57.60        61.87        30.51 
TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2043 TCGA-09-2044 
        5.85         3.02         8.55        97.55         6.18         6.12 
TCGA-09-2048 TCGA-09-2049 TCGA-09-2050 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 
        4.54       112.41        71.11        39.75        20.94        26.93 
TCGA-09-2056 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0936 
       12.46        81.47        18.51        33.24        32.28        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0720 TCGA-13-0724 TCGA-13-0726 
       15.12        19.86         6.21        44.55         2.73        31.10 
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 
       31.04        21.40        38.93        36.72        30.35        19.59 
TCGA-13-0797 TCGA-13-0800 TCGA-13-0801 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 
        8.71         8.12         8.28        43.86        35.28        35.28 
TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 
       13.61        68.94       107.18        91.40        74.27        66.67 
TCGA-13-0890 TCGA-13-0899 TCGA-13-0900 TCGA-13-0903 TCGA-13-0905 TCGA-13-0906 
       67.99        56.15        57.07        47.38        47.84        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0920 
       44.84        37.08        27.72        34.06        29.98        13.81 
TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 
        6.41         6.08        10.88         6.61         7.36         6.05 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1483 TCGA-13-1484 
        5.92         6.84         4.21         5.33        29.42        98.04 
TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1495 TCGA-13-1497 TCGA-13-1498 
       22.39        70.82        82.88        49.25        54.31        37.61 
TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 
       38.40        13.97        32.84         4.21         4.41         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 
        4.18         3.91         3.09        14.24        12.23         8.61 
TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
       10.78         8.75         6.28        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-23-1023 TCGA-23-1027 TCGA-23-1028 TCGA-23-1030 
       47.54        42.54        40.54        31.76        49.41        29.13 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 
        3.22        31.20        68.68         4.57        33.30        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-23-2072 TCGA-23-2078 TCGA-23-2079 TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 
       24.95        87.48        91.66        77.00        49.84         4.70 
TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 TCGA-24-0979 TCGA-24-0982 TCGA-24-1104 
        4.50         7.63        11.64        41.56        22.32        63.55 
TCGA-24-1413 TCGA-24-1416 TCGA-24-1417 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 
        6.31         6.38         7.82         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        19.17 
TCGA-24-1435 TCGA-24-1436 TCGA-24-1463 TCGA-24-1464 TCGA-24-1470 TCGA-24-1471 
       43.53         8.55        72.92        12.46         3.45         1.18 
TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1552 TCGA-24-1555 
       22.22        57.40        64.27        16.21        41.39        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-24-1567 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1842 
       25.87        17.23        90.15        88.37        48.33         8.32 
TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 TCGA-24-1847 TCGA-24-1849 TCGA-24-1850 
        3.48         3.72         4.37        11.28         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 
        9.80        22.68        30.21        16.44        11.05       152.02 
TCGA-24-2023 TCGA-24-2024 TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2035 
       44.84        58.16       109.71        14.43        53.95        28.18 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2261 TCGA-24-2267 TCGA-24-2271 TCGA-24-2288 
       64.01        57.07         0.79        47.54        31.63         0.82 
TCGA-24-2289 TCGA-24-2293 TCGA-24-2297 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 
       67.36        16.64        55.86         1.02        32.02        51.06 
TCGA-25-1316 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
       37.02         1.02        34.98        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 
       12.00         2.96        18.02        15.81         0.36        20.61 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 
       56.94        60.59        35.54        18.05        85.05        13.02 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2399 TCGA-25-2401 TCGA-25-2404 TCGA-25-2409 
        1.02        38.04        19.99         2.96        29.03        26.99 
TCGA-29-1691 TCGA-29-1693 TCGA-29-1694 TCGA-29-1697 TCGA-29-1701 TCGA-29-1702 
       47.18       101.79        38.53        31.20        16.90        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1763 TCGA-29-1764 TCGA-29-1768 
       59.67        18.25        41.98        66.81        62.93        31.23 
TCGA-29-1769 TCGA-29-1770 TCGA-29-1775 TCGA-29-1777 TCGA-29-1781 TCGA-29-1783 
       22.98        24.36        12.36        12.30         8.38         7.23 
TCGA-29-1784 TCGA-29-2414 TCGA-29-2425 TCGA-29-2427 TCGA-29-2428 TCGA-29-2429 
        5.36        86.17        65.00        62.47        45.11         4.90 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 
       11.47        21.04        38.07        51.91        36.26        15.68 
TCGA-30-1861 TCGA-30-1866 TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-31-1944 
       34.78        36.62         1.22        57.57        30.05        45.57 
TCGA-31-1946 TCGA-31-1951 TCGA-31-1955 TCGA-31-1956 TCGA-31-1959 TCGA-36-1570 
       30.18        22.49        42.51        44.12         2.20        21.53 
TCGA-36-1571 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       22.85        22.55         8.55        25.74        27.85        24.23 
TCGA-36-2532 TCGA-36-2534 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 
       29.49        29.82        25.08        21.60         2.24        20.98 
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        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 TCGA-59-2350 
       11.38        21.14         1.74        29.00        25.08        22.32 
TCGA-59-2351 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-59-A5PD 
      116.12        34.39         2.14         5.42        44.81        20.52 
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         8.05 

$`DEL PEAK 32(18Q23) WILD-TYPE`
TCGA-04-1331 TCGA-04-1337 TCGA-04-1342 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 
       40.24         2.01        18.51        71.47        82.39        56.55 
TCGA-04-1525 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 TCGA-04-1648 TCGA-04-1649 
       38.37        29.10        84.20        55.43        28.64        64.64 
TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 
       29.16         9.47        57.76        35.57         9.99        38.43 
TCGA-09-1662 TCGA-09-1664 TCGA-09-1668 TCGA-09-1670 TCGA-09-2045 TCGA-09-2051 
       89.33        74.93        55.36        17.98        35.15        63.09 
TCGA-10-0925 TCGA-10-0926 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 TCGA-13-0717 
       54.31        25.91        11.70         3.91        35.44        24.59 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0768 
       39.58        12.39        11.38        34.06        32.25         8.45 
TCGA-13-0793 TCGA-13-0799 TCGA-13-0802 TCGA-13-0888 TCGA-13-0889 TCGA-13-0891 
       28.70         7.79         8.19        70.39        61.84        69.01 
TCGA-13-0893 TCGA-13-0897 TCGA-13-0901 TCGA-13-0904 TCGA-13-0916 TCGA-13-0919 
       43.36        57.47        19.36        48.33        21.17        14.89 
TCGA-13-0921 TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1482 TCGA-13-1485 
        4.64         4.70        54.64        87.06        61.71        20.68 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1504 TCGA-13-1510 
       52.44        73.55        38.20         4.24        16.57         2.56 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 TCGA-23-1024 TCGA-23-1026 TCGA-23-1029 
       54.77         8.42        72.20        15.39        26.83         8.81 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1109 TCGA-23-1110 TCGA-23-1121 TCGA-23-2077 
       18.90         2.24        51.35        54.51         6.38       115.89 
TCGA-23-2641 TCGA-24-0968 TCGA-24-0975 TCGA-24-0980 TCGA-24-1103 TCGA-24-1105 
        2.76        19.66        21.80         7.66        54.12        47.41 
TCGA-24-1419 TCGA-24-1430 TCGA-24-1434 TCGA-24-1466 TCGA-24-1467 TCGA-24-1469 
        7.86        28.37        18.67        45.14       105.99         9.11 
TCGA-24-1544 TCGA-24-1549 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1565 
       26.96        56.58        41.06        51.91        58.09        10.26 
TCGA-24-1616 TCGA-24-1845 TCGA-24-1930 TCGA-24-2019 TCGA-24-2026 TCGA-24-2033 
       38.24         3.81        81.11         4.87        34.82        18.48 
TCGA-24-2038 TCGA-24-2260 TCGA-24-2262 TCGA-24-2280 TCGA-24-2281 TCGA-24-2290 
       44.52        36.16         0.36        70.45        44.61        36.23 
TCGA-24-2295 TCGA-24-2298 TCGA-25-1313 TCGA-25-1319 TCGA-25-1623 TCGA-25-1630 
       33.11        53.26        26.96        65.00        18.58         7.86 
TCGA-25-1631 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-2391 TCGA-25-2396 
        0.30        51.22        14.96        24.99        49.05         3.02 
TCGA-25-2397 TCGA-25-2398 TCGA-25-2400 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 
       12.00        45.01        42.02        31.00        78.90        44.71 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1698 TCGA-29-1699 TCGA-29-1710 TCGA-29-1711 
        0.79        33.70        68.32         0.53        29.23        34.62 
TCGA-29-1761 TCGA-29-1762 TCGA-29-1766 TCGA-29-1771 TCGA-29-1774 TCGA-29-1776 
       17.00        85.68        39.12        22.55        17.33        11.84 
TCGA-29-1778 TCGA-29-1785 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-30-1855 
       14.93        34.62        42.25        11.84         9.76         2.47 
TCGA-30-1857 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1887 TCGA-30-1892 
        0.26        48.10        44.91         6.12        24.26        48.79 
TCGA-31-1950 TCGA-31-1953 TCGA-36-1568 TCGA-36-1569 TCGA-36-1576 TCGA-36-1581 
       18.77         6.71        28.77        29.10        30.08        24.69 
TCGA-36-2529 TCGA-36-2530 TCGA-36-2537 TCGA-36-2540 TCGA-36-2545 TCGA-36-2551 
       35.05        33.01        25.91        23.80        18.31        16.18 
TCGA-3P-A9WA TCGA-57-1586 TCGA-57-1994 TCGA-59-2348 TCGA-59-2349 TCGA-59-2352 
        7.99        22.32        25.02       180.20        80.12         9.40 
TCGA-61-1721 TCGA-61-1733 TCGA-61-1734 TCGA-61-1737 TCGA-61-1738 TCGA-61-1895 
       11.11        31.79        28.47        44.84        35.80         1.45 
TCGA-61-1899 TCGA-61-1903 TCGA-61-1910 TCGA-61-1913 TCGA-61-1917 TCGA-61-1918 
        8.42        13.02        37.05        48.92        43.43        15.75 
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-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 TCGA-61-2098 
        1.18        45.96         4.80        51.72        61.64        65.52 
TCGA-61-2101 TCGA-61-2113 TCGA-61-2614 TCGA-OY-A56Q 
       55.50        22.22         8.61        18.94 

  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                        0.36                         0.26 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      152.02                       180.20 
  DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE 
                      26.565                       29.130 
[1] "0.4 - 152.0 (26.6)" "0.3 - 180.2 (29.1)"
[1] "hr=" "1"  
D65V2, continuous
                              vv
clus                           OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 32(18Q23) MUTATED         1   367                0
  DEL PEAK 32(18Q23) WILD-TYPE       1   190                2
D65V3, multiclass
                  clus
vv                 DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  OMENTUM                                   1                            1
  OVARY                                   367                          190
  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"
D65V4, continuous
D65V5, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED     2 374
  DEL PEAK 32(18Q23) WILD-TYPE   1 194
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED      2  374
  DEL PEAK 32(18Q23) WILD-TYPE    1  194
     clus
vv    DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  NO                           2                            1
  YES                        374                          194
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 32(18Q23) MUTATED   11 18  4  0
  DEL PEAK 32(18Q23) WILD-TYPE  3  8  1  3
D65V6, multiclass
    clus
vv   DEL PEAK 32(18Q23) MUTATED DEL PEAK 32(18Q23) WILD-TYPE
  R0                         11                            3
  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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(18Q23) MUTATED                                  3     9
  DEL PEAK 32(18Q23) WILD-TYPE                                0     9
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(18Q23) MUTATED                          18
  DEL PEAK 32(18Q23) WILD-TYPE                        14
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 32(18Q23) MUTATED                                           1   315
  DEL PEAK 32(18Q23) WILD-TYPE                                         0   160
D65V7, multiclass
                                           clus
vv                                          DEL PEAK 32(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   3
  ASIAN                                                              9
  BLACK OR AFRICAN AMERICAN                                         18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                            315
                                           clus
vv                                          DEL PEAK 32(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                9
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              160
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                              cls
clus                             0   1
  DEL PEAK 32(18Q23) MUTATED     7 216
  DEL PEAK 32(18Q23) WILD-TYPE   3 109
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 32(18Q23) MUTATED      7  216
  DEL PEAK 32(18Q23) WILD-TYPE    3  109
                        clus
vv                       DEL PEAK 32(18Q23) MUTATED
  HISPANIC OR LATINO                              7
  NOT HISPANIC OR LATINO                        216
                        clus
vv                       DEL PEAK 32(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          109
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 33(19P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(19P13.3) MUTATED   237 253
  DEL PEAK 33(19P13.3) WILD-TYPE  29  37
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           490                             66 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                           253                             37 
$`DEL PEAK 33(19P13.3) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1335 TCGA-04-1336 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00         1.81        49.15        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 
       11.87        65.52        63.09        21.57        63.98        65.46 
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        71.47 
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-04-1651 TCGA-04-1652 TCGA-04-1655 TCGA-09-0364 TCGA-09-0366 
       64.64        36.23        31.86        45.37        29.16        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1665 
       17.98        35.57         9.99        38.43        74.93        41.62 
TCGA-09-1666 TCGA-09-1667 TCGA-09-1668 TCGA-09-1669 TCGA-09-1670 TCGA-09-1672 
       57.60        61.87        55.36        30.51        17.98         5.85 
TCGA-09-1673 TCGA-09-1674 TCGA-09-2044 TCGA-09-2045 TCGA-09-2049 TCGA-09-2050 
        3.02         8.55         6.12        35.15       112.41        71.11 
TCGA-09-2051 TCGA-09-2053 TCGA-09-2054 TCGA-09-2055 TCGA-09-2056 TCGA-10-0926 
       63.09        39.75        20.94        26.93        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       81.47        18.51        32.28        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       35.80        15.12        19.86         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-13-0755 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0762 TCGA-13-0766 
        2.50        11.18        11.38        34.06        32.25        21.40 
TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 TCGA-13-0795 
        8.45        38.93        36.72        28.70        30.35        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 
        8.71         7.79         8.12         8.28         8.19        43.86 
TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 TCGA-13-0885 
       35.28        35.28        13.61        68.94       107.18        91.40 
TCGA-13-0886 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 TCGA-13-0893 
       74.27        70.39        61.84        67.99        69.01        43.36 
TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0906 
       56.15        57.07        19.36        47.38        48.33        44.94 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 TCGA-13-0916 
       44.84        37.08        27.72        34.06        29.98        21.17 
TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 TCGA-13-1403 
       14.89        13.81         4.64         6.41         6.08        10.88 
TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 
        6.61         7.36         6.05         5.92         6.84         4.70 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 
        4.21         5.33        87.06        61.71        29.42        22.39 
TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 
       70.82        82.88        52.44        73.55        38.20        49.25 
TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 
        4.24        37.61        38.40        13.97        32.84        16.57 
TCGA-13-1505 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 
        4.21         4.41         4.77         4.18         2.56         3.91 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        3.09        14.24        12.23         8.61        10.78         8.75 
TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 
        6.28        54.77         8.42        23.05        25.94        26.20 
TCGA-20-1683 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1023 
       25.38        19.10        16.70         2.93         2.66        40.54 
TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 
       15.39        31.76        49.41         8.81        29.13        18.90 
TCGA-23-1032 TCGA-23-1110 TCGA-23-1111 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 
        2.24        54.51         3.22        31.20        68.68         4.57 
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-23-1124 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-23-2081 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-24-0968 TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 
       19.66        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        19.17        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        53.95 
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 
       32.02        51.06        37.02         1.02        34.98        65.00 
TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
       36.95        33.96         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1631 TCGA-25-1632 
       18.02        15.81         0.36        20.61         0.30        56.94 
TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 
       60.59        35.54        51.22        14.96        24.99        18.05 
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        47.18       101.79        38.53         0.79        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 TCGA-29-1703 TCGA-29-1705 
       31.20        68.32         0.53        16.90        59.67        18.25 
TCGA-29-1707 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       41.98        29.23        34.62        17.00        85.68        66.81 
TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 TCGA-29-1771 
       62.93        39.12        31.23        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        34.62        86.17        62.47        45.11         4.90 
TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 
       42.25        11.84        11.47        21.04        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-3P-A9WA TCGA-42-2582 TCGA-42-2588 TCGA-42-2591 
       16.18        11.47         7.99        26.04         9.44        40.77 
TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 
       24.03        11.38        21.14         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-59-2372 TCGA-59-A5PD TCGA-61-1722 
       34.39         2.14         5.42        44.81        20.52         8.09 
TCGA-61-1724 TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1734 
       20.94        31.43        27.88         4.34        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-61-1899 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-61-1911 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-61-1919 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 
       38.17         2.01        14.50        17.98         4.01        30.64 
TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 
       30.64         1.18        45.40         4.77        71.74        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-OY-A56P TCGA-OY-A56Q TCGA-VG-A8LO TCGA-WR-A838 
       39.68        18.94         0.79         8.05 

$`DEL PEAK 33(19P13.3) WILD-TYPE`
TCGA-04-1337 TCGA-04-1348 TCGA-04-1654 TCGA-09-0365 TCGA-09-1662 TCGA-09-1675 
        2.01        48.76        47.70         9.47        89.33        97.55 
TCGA-09-2043 TCGA-09-2048 TCGA-10-0925 TCGA-10-0930 TCGA-13-0726 TCGA-13-0760 
        6.18         4.54        54.31        33.24        31.10        11.54 
TCGA-13-0764 TCGA-13-0887 TCGA-13-0897 TCGA-13-0905 TCGA-13-1477 TCGA-13-1484 
       31.04        66.67        57.47        47.84        54.64        98.04 
TCGA-13-1485 TCGA-13-1497 TCGA-20-0996 TCGA-20-1682 TCGA-23-1021 TCGA-23-1022 
       20.68        54.31        72.20        27.52        47.54        42.54 
TCGA-23-1026 TCGA-23-1109 TCGA-23-2079 TCGA-24-0980 TCGA-24-1423 TCGA-24-1553 
       26.83        51.35        91.66         7.66         6.25        58.09 
TCGA-24-1603 TCGA-24-1604 TCGA-24-1842 TCGA-24-1930 TCGA-24-2038 TCGA-24-2254 
       90.15        88.37         8.32        81.11        44.52        57.07 
TCGA-24-2271 TCGA-25-1630 TCGA-25-2408 TCGA-29-1688 TCGA-29-1690 TCGA-29-1702 
       31.63         7.86        31.00        78.90        44.71        18.67 
TCGA-29-1775 TCGA-29-2425 TCGA-29-2436 TCGA-30-1862 TCGA-30-1880 TCGA-31-1946 
       12.36        65.00         9.76         6.12        57.57        30.18 
TCGA-36-2540 TCGA-36-2542 TCGA-42-2587 TCGA-42-2589 TCGA-42-2590 TCGA-42-2593 
       23.80        21.60        23.74        42.02         7.46         1.48 
TCGA-59-2349 TCGA-61-1721 TCGA-61-1727 TCGA-61-1901 TCGA-61-1910 TCGA-61-1918 
       80.12        11.11        18.54        11.41        37.05        15.75 
TCGA-61-1998 TCGA-61-2009 TCGA-61-2017 TCGA-61-2087 TCGA-61-2092 TCGA-61-2095 
        5.52        39.85        45.96         4.80        51.72        61.64 

  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                          0.26                           1.48 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        180.20                          98.04 
  DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE 
                        26.960                         35.145 
[1] "0.3 - 180.2 (27.0)" "1.5 - 98.0 (35.1)" 
[1] "hr=" "1.2"
D66V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 33(19P13.3) MUTATED         2   490                2
  DEL PEAK 33(19P13.3) WILD-TYPE       0    67                0
D66V3, multiclass
                  clus
vv                 DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  OMENTUM                                     2                              0
  OVARY                                     490                             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"
D66V4, continuous
D66V5, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED     3 501
  DEL PEAK 33(19P13.3) WILD-TYPE   0  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED      3  501
  DEL PEAK 33(19P13.3) WILD-TYPE    0   67
     clus
vv    DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  NO                             3                              0
  YES                          501                             67
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 33(19P13.3) MUTATED   12 21  4  3
  DEL PEAK 33(19P13.3) WILD-TYPE  2  5  1  0
D66V6, multiclass
    clus
vv   DEL PEAK 33(19P13.3) MUTATED DEL PEAK 33(19P13.3) WILD-TYPE
  R0                           12                              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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(19P13.3) MUTATED                                  2    16
  DEL PEAK 33(19P13.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(19P13.3) MUTATED                          32
  DEL PEAK 33(19P13.3) WILD-TYPE                         0
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 33(19P13.3) MUTATED                                           1
  DEL PEAK 33(19P13.3) WILD-TYPE                                         0
                                vv
clus                             WHITE
  DEL PEAK 33(19P13.3) MUTATED     415
  DEL PEAK 33(19P13.3) WILD-TYPE    60
D66V7, multiclass
                                           clus
vv                                          DEL PEAK 33(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                           32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                              415
                                           clus
vv                                          DEL PEAK 33(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       1
  ASIAN                                                                  2
  BLACK OR AFRICAN AMERICAN                                              0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              0
  WHITE                                                                 60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(19P13.3) MUTATED     9 282
  DEL PEAK 33(19P13.3) WILD-TYPE   1  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(19P13.3) MUTATED      9  282
  DEL PEAK 33(19P13.3) WILD-TYPE    1   43
                        clus
vv                       DEL PEAK 33(19P13.3) MUTATED
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          282
                        clus
vv                       DEL PEAK 33(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             43
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 34(19Q13.33) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 34(19Q13.33) MUTATED   144 143
  DEL PEAK 34(19Q13.33) WILD-TYPE 122 147
  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                            287                             269 
  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                            143                             147 
$`DEL PEAK 34(19Q13.33) MUTATED`
TCGA-04-1335 TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 
        1.81        48.76        21.57        63.98        49.28        44.32 
TCGA-04-1365 TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1525 
       76.57        71.47        82.39        56.55        41.59        38.37 
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-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0366 TCGA-09-1659 
       64.64        31.86        47.70        45.37        57.76         9.99 
TCGA-09-1661 TCGA-09-1664 TCGA-09-1665 TCGA-09-1667 TCGA-09-1668 TCGA-09-1672 
       38.43        74.93        41.62        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-10-0925 
       63.09        39.75        20.94        26.93        12.46        54.31 
TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 TCGA-10-0934 TCGA-10-0936 
       25.91        81.47        18.51        32.28         3.91        35.80 
TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 TCGA-13-0726 TCGA-13-0730 
       15.12        19.86        39.58         2.73        31.10        17.82 
TCGA-13-0751 TCGA-13-0755 TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 
       55.17         2.50        11.54        34.06        32.25        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0792 TCGA-13-0794 TCGA-13-0797 TCGA-13-0799 
       21.40         8.45        36.72        30.35         8.71         7.79 
TCGA-13-0800 TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0886 
        8.12        43.86        35.28        35.28        13.61        74.27 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0903 TCGA-13-0908 TCGA-13-0911 TCGA-13-0913 
       57.47        56.15        47.38        44.84        27.72        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0921 TCGA-13-0923 TCGA-13-1403 TCGA-13-1404 
       21.17        14.89         4.64         6.41        10.88         6.61 
TCGA-13-1407 TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 
        6.05         4.21         5.33        87.06        29.42        98.04 
TCGA-13-1487 TCGA-13-1489 TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 
       22.39        82.88        52.44        38.20        49.25         4.24 
TCGA-13-1497 TCGA-13-1498 TCGA-13-1499 TCGA-13-1505 TCGA-13-1506 TCGA-13-1510 
       54.31        37.61        38.40         4.21         4.41         2.56 
TCGA-13-2059 TCGA-13-2060 TCGA-13-2065 TCGA-13-2071 TCGA-20-0990 TCGA-20-0991 
       12.23         8.61         8.75         6.28        25.94        26.20 
TCGA-20-1682 TCGA-20-1684 TCGA-20-1685 TCGA-20-1686 TCGA-20-1687 TCGA-23-1021 
       27.52        19.10        16.70         2.93         2.66        47.54 
TCGA-23-1022 TCGA-23-1024 TCGA-23-1026 TCGA-23-1028 TCGA-23-1030 TCGA-23-1032 
       42.54        15.39        26.83        49.41        29.13         2.24 
TCGA-23-1110 TCGA-23-1118 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-1124 
       54.51        86.01       129.96         6.38        33.47        58.13 
TCGA-23-2072 TCGA-23-2077 TCGA-23-2079 TCGA-23-2081 TCGA-23-2641 TCGA-23-2643 
       24.95       115.89        91.66        77.00         2.76         4.70 
TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 TCGA-24-1413 
        7.63        19.66        41.56         7.66        22.32         6.31 
TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1434 TCGA-24-1435 
        0.76         6.25         6.02         5.36        18.67        43.53 
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-24-1474 TCGA-24-1548 TCGA-24-1549 TCGA-24-1552 TCGA-24-1556 TCGA-24-1558 
       22.22        16.21        56.58        41.39        70.62        19.53 
TCGA-24-1560 TCGA-24-1564 TCGA-24-1565 TCGA-24-1603 TCGA-24-1614 TCGA-24-1843 
       44.09        25.87        10.26        90.15        48.33         3.48 
TCGA-24-1844 TCGA-24-1846 TCGA-24-1920 TCGA-24-1930 TCGA-24-2019 TCGA-24-2023 
        3.72         4.37         9.80        81.11         4.87        44.84 
TCGA-24-2024 TCGA-24-2026 TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2280 
       58.16        34.82        64.01        57.07        36.16        70.45 
TCGA-24-2281 TCGA-24-2293 TCGA-25-1312 TCGA-25-1316 TCGA-25-1319 TCGA-25-1320 
       44.61        16.64         1.02        37.02        65.00        36.95 
TCGA-25-1321 TCGA-25-1627 TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 
       33.96         0.36         0.30        56.94        60.59        35.54 
TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2391 
       51.22        14.96        24.99        18.05        85.05        49.05 
TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 
        1.02        38.04         3.02        19.99        42.02        26.99 
TCGA-29-1691 TCGA-29-1694 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1702 
       47.18        38.53        31.20        68.32         0.53        18.67 
TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 TCGA-29-1710 TCGA-29-1763 TCGA-29-1771 
       59.67        18.25        41.98        29.23        66.81        22.55 
TCGA-29-1775 TCGA-29-1778 TCGA-29-1784 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 
       12.36        14.93         5.36        65.00        62.47        42.25 
TCGA-29-2434 TCGA-30-1714 TCGA-30-1853 TCGA-30-1855 TCGA-30-1857 TCGA-30-1861 
       11.47        38.07        36.26         2.47         0.26        34.78 
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-31-1953 TCGA-31-1956 TCGA-36-1569 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
        6.71        44.12        29.10        22.85        22.55        30.08 
TCGA-36-1577 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2530 TCGA-36-2534 
       25.74        24.23        24.69        35.05        33.01        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2547 TCGA-36-2551 
       25.91        25.08        21.60         2.24        20.52        16.18 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2589 TCGA-42-2590 TCGA-57-1583 
       11.47         7.99        26.04        42.02         7.46        11.38 
TCGA-57-1584 TCGA-57-1993 TCGA-57-1994 TCGA-59-2355 TCGA-59-2372 TCGA-61-1724 
       21.14        25.08        25.02         2.14        44.81        20.94 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1730 TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 
       31.43        27.88         4.34        31.79        35.80        33.67 
TCGA-61-1895 TCGA-61-1899 TCGA-61-1901 TCGA-61-1907 TCGA-61-1915 TCGA-61-1917 
        1.45         8.42        11.41        31.30        67.76        43.43 
TCGA-61-1918 TCGA-61-1995 TCGA-61-2000 TCGA-61-2002 TCGA-61-2003 TCGA-61-2012 
       15.75         2.01        14.50        17.98         4.01        30.64 
TCGA-61-2016 TCGA-61-2017 TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 
        1.18        45.96         4.80         4.77        71.74        58.39 
TCGA-61-2102 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P TCGA-OY-A56Q 
        6.48         6.35         8.61        39.68        18.94 

$`DEL PEAK 34(19Q13.33) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1361 TCGA-04-1364 
       11.87        65.52        63.09        65.46        32.52        33.67 
TCGA-04-1517 TCGA-04-1646 TCGA-04-1651 TCGA-09-0364 TCGA-09-0365 TCGA-09-0367 
       19.99        27.88        36.23        29.16         9.47        17.98 
TCGA-09-0369 TCGA-09-1662 TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-2043 
       35.57        89.33        57.60        30.51        17.98         6.18 
TCGA-09-2044 TCGA-09-2045 TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-13-0714 
        6.12        35.15        33.24        11.70        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 
       38.93        28.70        19.59         8.28         8.19        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 
      107.18        91.40        66.67        70.39        61.84        67.99 
TCGA-13-0891 TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 
       69.01        43.36        57.07        19.36        48.33        47.84 
TCGA-13-0906 TCGA-13-0910 TCGA-13-0912 TCGA-13-0920 TCGA-13-0924 TCGA-13-1405 
       44.94        37.08        34.06        13.81         6.08         7.36 
TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1482 TCGA-13-1485 
        5.92         6.84         4.70        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        73.55        13.97        32.84        16.57         4.77 
TCGA-13-1509 TCGA-13-1511 TCGA-13-1512 TCGA-13-2057 TCGA-13-2061 TCGA-13-A5FT 
        4.18         3.91         3.09        14.24        10.78        54.77 
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        31.76 
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 
        4.57        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        19.17         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        53.95        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        32.02        51.06 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1322 TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 
        1.02        34.98         2.99        12.00         2.96        18.58 
TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 TCGA-25-2042 TCGA-25-2397 
       18.02        15.81        20.61         7.86        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        44.71 
TCGA-29-1693 TCGA-29-1695 TCGA-29-1696 TCGA-29-1701 TCGA-29-1711 TCGA-29-1761 
      101.79         0.79        33.70        16.90        34.62        17.00 
TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1770 
       85.68        62.93        39.12        31.23        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        34.62 
TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ 
       86.17        45.11         4.90        11.84         9.76        21.04 
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         9.44        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-59-A5PD TCGA-61-1721 TCGA-61-1722 TCGA-61-1727 TCGA-61-1734 TCGA-61-1736 
       20.52        11.11         8.09        18.54        28.47        48.79 
TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 TCGA-61-1900 TCGA-61-1903 TCGA-61-1904 
       44.84         2.43        43.69         5.79        13.02         9.07 
TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1919 
       34.13        37.05        42.51        48.92        56.61        38.17 
TCGA-61-1998 TCGA-61-2008 TCGA-61-2009 TCGA-61-2018 TCGA-61-2092 TCGA-61-2095 
        5.52        30.64        39.85        45.40        51.72        61.64 
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-VG-A8LO TCGA-WR-A838 
      125.75        22.22        31.07         0.79         8.05 

  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                           0.26                            0.36 
  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                         129.96                          180.20 
  DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE 
                          28.64                           27.88 
[1] "0.3 - 130.0 (28.6)" "0.4 - 180.2 (27.9)"
[1] "hr=" "1.1"
D67V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 34(19Q13.33) MUTATED         1   287                1
  DEL PEAK 34(19Q13.33) WILD-TYPE       1   270                1
D67V3, multiclass
                  clus
vv                 DEL PEAK 34(19Q13.33) MUTATED
  OMENTUM                                      1
  OVARY                                      287
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 34(19Q13.33) WILD-TYPE
  OMENTUM                                        1
  OVARY                                        270
  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"
D67V4, continuous
D67V5, binary
                                 cls
clus                                0   1
  DEL PEAK 34(19Q13.33) MUTATED     3 291
  DEL PEAK 34(19Q13.33) WILD-TYPE   0 277
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(19Q13.33) MUTATED      3  291
  DEL PEAK 34(19Q13.33) WILD-TYPE    0  277
     clus
vv    DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE
  NO                              3                               0
  YES                           291                             277
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 34(19Q13.33) MUTATED    9 16  1  2
  DEL PEAK 34(19Q13.33) WILD-TYPE  5 10  4  1
D67V6, multiclass
    clus
vv   DEL PEAK 34(19Q13.33) MUTATED DEL PEAK 34(19Q13.33) WILD-TYPE
  R0                             9                               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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(19Q13.33) MUTATED                                  0     7
  DEL PEAK 34(19Q13.33) WILD-TYPE                                3    11
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(19Q13.33) MUTATED                          19
  DEL PEAK 34(19Q13.33) WILD-TYPE                        13
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(19Q13.33) MUTATED                                           0
  DEL PEAK 34(19Q13.33) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 34(19Q13.33) MUTATED     248
  DEL PEAK 34(19Q13.33) WILD-TYPE   227
D67V7, multiclass
                                           clus
vv                                          DEL PEAK 34(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               248
                                           clus
vv                                          DEL PEAK 34(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  11
  BLACK OR AFRICAN AMERICAN                                              13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 227
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                                 cls
clus                                0   1
  DEL PEAK 34(19Q13.33) MUTATED     8 171
  DEL PEAK 34(19Q13.33) WILD-TYPE   2 154
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(19Q13.33) MUTATED      8  171
  DEL PEAK 34(19Q13.33) WILD-TYPE    2  154
                        clus
vv                       DEL PEAK 34(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           171
                        clus
vv                       DEL PEAK 34(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             154
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 35(19Q13.43) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(19Q13.43) MUTATED   132 141
  DEL PEAK 35(19Q13.43) WILD-TYPE 134 149
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            273                             283 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            141                             149 
$`DEL PEAK 35(19Q13.43) MUTATED`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1346 TCGA-04-1347 TCGA-04-1348 TCGA-04-1349 
        1.81        49.15        65.52        63.09        48.76        21.57 
TCGA-04-1350 TCGA-04-1356 TCGA-04-1362 TCGA-04-1364 TCGA-04-1365 TCGA-04-1367 
       63.98        49.28        44.32        33.67        76.57        71.47 
TCGA-04-1371 TCGA-04-1516 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1638 
       82.39        41.59        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-09-0365 TCGA-09-0366 TCGA-09-1659 TCGA-09-1661 TCGA-09-1664 TCGA-09-1667 
        9.47        57.76         9.99        38.43        74.93        61.87 
TCGA-09-1668 TCGA-09-1672 TCGA-09-1673 TCGA-09-1674 TCGA-09-1675 TCGA-09-2048 
       55.36         5.85         3.02         8.55        97.55         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0931 
       12.46        54.31        25.91        81.47        18.51        32.28 
TCGA-10-0934 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0723 TCGA-13-0724 
        3.91        35.80        15.12        19.86        39.58         2.73 
TCGA-13-0726 TCGA-13-0730 TCGA-13-0751 TCGA-13-0755 TCGA-13-0757 TCGA-13-0760 
       31.10        17.82        55.17         2.50        11.18        11.54 
TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0768 TCGA-13-0794 
       34.06        32.25        31.04        21.40         8.45        30.35 
TCGA-13-0795 TCGA-13-0799 TCGA-13-0800 TCGA-13-0804 TCGA-13-0807 TCGA-13-0886 
       19.59         7.79         8.12        35.28        13.61        74.27 
TCGA-13-0888 TCGA-13-0897 TCGA-13-0899 TCGA-13-0903 TCGA-13-0908 TCGA-13-0911 
       70.39        57.47        56.15        47.38        44.84        27.72 
TCGA-13-0912 TCGA-13-0919 TCGA-13-0921 TCGA-13-1403 TCGA-13-1404 TCGA-13-1407 
       34.06        14.89         4.64        10.88         6.61         6.05 
TCGA-13-1411 TCGA-13-1412 TCGA-13-1481 TCGA-13-1483 TCGA-13-1484 TCGA-13-1489 
        4.21         5.33        87.06        29.42        98.04        82.88 
TCGA-13-1491 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1498 TCGA-13-1499 
       52.44        38.20        49.25         4.24        37.61        38.40 
TCGA-13-1505 TCGA-13-1510 TCGA-13-2057 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 
        4.21         2.56        14.24         8.61        10.78         8.75 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1684 TCGA-20-1686 
       23.05        25.94        26.20        27.52        19.10         2.93 
TCGA-20-1687 TCGA-23-1021 TCGA-23-1030 TCGA-23-1032 TCGA-23-1110 TCGA-23-1119 
        2.66        47.54        29.13         2.24        54.51       129.96 
TCGA-23-1121 TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-2079 TCGA-23-2081 
        6.38        39.09        33.47        58.13        91.66        77.00 
TCGA-23-2643 TCGA-24-0966 TCGA-24-0968 TCGA-24-0979 TCGA-24-0980 TCGA-24-0982 
        4.70         7.63        19.66        41.56         7.66        22.32 
TCGA-24-1413 TCGA-24-1424 TCGA-24-1426 TCGA-24-1434 TCGA-24-1435 TCGA-24-1463 
        6.31         6.02         5.36        18.67        43.53        72.92 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1549 TCGA-24-1552 
       12.46       105.99         9.11         3.45        56.58        41.39 
TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 TCGA-24-1560 TCGA-24-1563 TCGA-24-1564 
       88.50        70.62        19.53        44.09        47.70        25.87 
TCGA-24-1565 TCGA-24-1603 TCGA-24-1604 TCGA-24-1614 TCGA-24-1843 TCGA-24-1844 
       10.26        90.15        88.37        48.33         3.48         3.72 
TCGA-24-1846 TCGA-24-1847 TCGA-24-1930 TCGA-24-2019 TCGA-24-2024 TCGA-24-2026 
        4.37        11.28        81.11         4.87        58.16        34.82 
TCGA-24-2029 TCGA-24-2260 TCGA-24-2280 TCGA-24-2281 TCGA-24-2288 TCGA-24-2293 
       14.43        36.16        70.45        44.61         0.82        16.64 
TCGA-24-2298 TCGA-25-1315 TCGA-25-1316 TCGA-25-1319 TCGA-25-1321 TCGA-25-1627 
       53.26        51.06        37.02        65.00        33.96         0.36 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-1878 TCGA-25-2392 TCGA-25-2393 TCGA-25-2396 
       24.99        18.05        85.05         1.02        38.04         3.02 
TCGA-25-2398 TCGA-25-2399 TCGA-25-2400 TCGA-25-2409 TCGA-29-1691 TCGA-29-1694 
       45.01        19.99        42.02        26.99        47.18        38.53 
TCGA-29-1695 TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1699 TCGA-29-1701 
        0.79        33.70        31.20        68.32         0.53        16.90 
TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 
       18.67        59.67        18.25        29.23        34.62        17.00 
TCGA-29-1762 TCGA-29-1768 TCGA-29-1771 TCGA-29-1774 TCGA-29-1775 TCGA-29-1778 
       85.68        31.23        22.55        17.33        12.36        14.93 
TCGA-29-1784 TCGA-29-2425 TCGA-29-2427 TCGA-29-2431 TCGA-29-2432 TCGA-29-2434 
        5.36        65.00        62.47        42.25        11.84        11.47 
TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1857 TCGA-30-1861 TCGA-30-1862 
       38.07        51.91        36.26         0.26        34.78         6.12 
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-31-1956 TCGA-36-1569 TCGA-36-1570 TCGA-36-1571 TCGA-36-1574 TCGA-36-1576 
       44.12        29.10        21.53        22.85        22.55        30.08 
TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2534 TCGA-36-2537 TCGA-36-2538 
       24.23        24.69        35.05        29.82        25.91        25.08 
TCGA-36-2542 TCGA-36-2547 TCGA-36-2551 TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2582 
       21.60        20.52        16.18        11.47         7.99        26.04 
TCGA-42-2589 TCGA-42-2590 TCGA-57-1584 TCGA-57-1993 TCGA-57-1994 TCGA-59-2355 
       42.02         7.46        21.14        25.08        25.02         2.14 
TCGA-59-2372 TCGA-59-A5PD TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81        20.52        31.43        18.54        27.88         4.34 
TCGA-61-1733 TCGA-61-1738 TCGA-61-1741 TCGA-61-1901 TCGA-61-1915 TCGA-61-1917 
       31.79        35.80        33.67        11.41        67.76        43.43 
TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 TCGA-61-2016 TCGA-61-2017 TCGA-61-2018 
       38.17        14.50        17.98         1.18        45.96        45.40 
TCGA-61-2087 TCGA-61-2088 TCGA-61-2094 TCGA-61-2096 TCGA-61-2097 TCGA-61-2102 
        4.80         4.77        71.74        58.39        60.62         6.48 
TCGA-61-2612 TCGA-OY-A56P TCGA-OY-A56Q 
        6.35        39.68        18.94 

$`DEL PEAK 35(19Q13.43) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       40.24        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-09-0364 TCGA-09-0367 TCGA-09-0369 TCGA-09-1662 TCGA-09-1665 
       36.23        29.16        17.98        35.57        89.33        41.62 
TCGA-09-1666 TCGA-09-1669 TCGA-09-1670 TCGA-09-2043 TCGA-09-2044 TCGA-09-2045 
       57.60        30.51        17.98         6.18         6.12        35.15 
TCGA-10-0930 TCGA-10-0933 TCGA-10-0935 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       33.24        11.70        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        38.93        36.72        28.70 
TCGA-13-0797 TCGA-13-0801 TCGA-13-0802 TCGA-13-0803 TCGA-13-0805 TCGA-13-0883 
        8.71         8.28         8.19        43.86        35.28        68.94 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0889 TCGA-13-0890 TCGA-13-0891 
      107.18        91.40        66.67        61.84        67.99        69.01 
TCGA-13-0893 TCGA-13-0900 TCGA-13-0901 TCGA-13-0904 TCGA-13-0905 TCGA-13-0906 
       43.36        57.07        19.36        48.33        47.84        44.94 
TCGA-13-0910 TCGA-13-0913 TCGA-13-0916 TCGA-13-0920 TCGA-13-0923 TCGA-13-0924 
       37.08        29.98        21.17        13.81         6.41         6.08 
TCGA-13-1405 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1477 TCGA-13-1482 
        7.36         5.92         6.84         4.70        54.64        61.71 
TCGA-13-1485 TCGA-13-1487 TCGA-13-1488 TCGA-13-1492 TCGA-13-1497 TCGA-13-1500 
       20.68        22.39        70.82        73.55        54.31        13.97 
TCGA-13-1501 TCGA-13-1504 TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1511 
       32.84        16.57         4.41         4.77         4.18         3.91 
TCGA-13-1512 TCGA-13-2059 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0996 
        3.09        12.23         6.28        54.77         8.42        72.20 
TCGA-20-1683 TCGA-20-1685 TCGA-23-1022 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 
       25.38        16.70        42.54        40.54        15.39        26.83 
TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1031 TCGA-23-1109 TCGA-23-1111 
       31.76        49.41         8.81        18.90        51.35         3.22 
TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 
       31.20        68.68         4.57        33.30        86.01         4.27 
TCGA-23-1809 TCGA-23-2072 TCGA-23-2077 TCGA-23-2078 TCGA-23-2084 TCGA-23-2641 
        0.53        24.95       115.89        87.48        49.84         2.76 
TCGA-23-2645 TCGA-24-0970 TCGA-24-0975 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 
        4.50        11.64        21.80        54.12        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-24-1425 TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1436 
        5.95         4.83        17.39        28.37        19.17         8.55 
TCGA-24-1466 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
       45.14         1.18        22.22        26.96        57.40        64.27 
TCGA-24-1548 TCGA-24-1550 TCGA-24-1551 TCGA-24-1553 TCGA-24-1557 TCGA-24-1562 
       16.21        41.06        51.91        58.09        39.88        45.50 
TCGA-24-1567 TCGA-24-1616 TCGA-24-1842 TCGA-24-1845 TCGA-24-1849 TCGA-24-1850 
       17.23        38.24         8.32         3.81         5.79         5.52 
TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-2020 
        9.80        22.68        30.21        16.44        11.05       152.02 
TCGA-24-2023 TCGA-24-2027 TCGA-24-2030 TCGA-24-2033 TCGA-24-2035 TCGA-24-2036 
       44.84       109.71        53.95        18.48        28.18        64.01 
TCGA-24-2038 TCGA-24-2254 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 TCGA-24-2271 
       44.52        57.07         0.79         0.36        47.54        31.63 
TCGA-24-2289 TCGA-24-2290 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 TCGA-25-1313 
       67.36        36.23        33.11        55.86         1.02        26.96 
TCGA-25-1314 TCGA-25-1317 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 TCGA-25-1323 
       32.02         1.02        34.98        36.95         2.99        12.00 
TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 TCGA-25-1630 
        2.96        18.58        18.02        15.81        20.61         7.86 
TCGA-25-2042 TCGA-25-2391 TCGA-25-2397 TCGA-25-2401 TCGA-25-2404 TCGA-25-2408 
       13.02        49.05        12.00         2.96        29.03        31.00 
TCGA-29-1688 TCGA-29-1690 TCGA-29-1693 TCGA-29-1707 TCGA-29-1763 TCGA-29-1764 
       78.90        44.71       101.79        41.98        66.81        62.93 
TCGA-29-1766 TCGA-29-1769 TCGA-29-1770 TCGA-29-1776 TCGA-29-1777 TCGA-29-1781 
       39.12        22.98        24.36        11.84        12.30         8.38 
TCGA-29-1783 TCGA-29-1785 TCGA-29-2414 TCGA-29-2428 TCGA-29-2429 TCGA-29-2436 
        7.23        34.62        86.17        45.11         4.90         9.76 
TCGA-29-A5NZ TCGA-30-1855 TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 
       21.04         2.47        15.68        48.10        44.91        36.62 
TCGA-30-1867 TCGA-30-1880 TCGA-30-1891 TCGA-30-1892 TCGA-31-1955 TCGA-31-1959 
        1.22        57.57        30.05        48.79        42.51         2.20 
TCGA-36-1568 TCGA-36-1575 TCGA-36-1577 TCGA-36-1578 TCGA-36-2530 TCGA-36-2532 
       28.77         8.55        25.74        27.85        33.01        29.49 
TCGA-36-2540 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 TCGA-36-2548 TCGA-36-2549 
       23.80         2.24        20.98        18.31        14.17         6.05 
TCGA-42-2587 TCGA-42-2588 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 
       23.74         9.44        40.77         1.48        24.03        11.38 
TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 
        1.74        22.32        29.00       180.20        80.12        22.32 
TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2363 TCGA-61-1721 TCGA-61-1722 
      116.12         9.40        34.39         5.42        11.11         8.09 
TCGA-61-1724 TCGA-61-1734 TCGA-61-1736 TCGA-61-1737 TCGA-61-1740 TCGA-61-1743 
       20.94        28.47        48.79        44.84         2.43        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-61-1910 TCGA-61-1911 TCGA-61-1913 TCGA-61-1914 TCGA-61-1918 
       31.30        37.05        42.51        48.92        56.61        15.75 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 
        2.01         5.52         4.01        30.64        39.85        30.64 
TCGA-61-2092 TCGA-61-2095 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2109 
       51.72        61.64        65.52        55.50        76.87        20.68 
TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 TCGA-61-2613 TCGA-61-2614 TCGA-VG-A8LO 
       44.52       125.75        22.22        31.07         8.61         0.79 
TCGA-WR-A838 
        8.05 

  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                           0.26                            0.36 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                         129.96                          180.20 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                          29.13                           26.96 
[1] "0.3 - 130.0 (29.1)" "0.4 - 180.2 (27.0)"
[1] "hr=" "1.1"
D68V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 35(19Q13.43) MUTATED         1   274                1
  DEL PEAK 35(19Q13.43) WILD-TYPE       1   283                1
D68V3, multiclass
                  clus
vv                 DEL PEAK 35(19Q13.43) MUTATED
  OMENTUM                                      1
  OVARY                                      274
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 35(19Q13.43) WILD-TYPE
  OMENTUM                                        1
  OVARY                                        283
  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"
D68V4, continuous
D68V5, binary
                                 cls
clus                                0   1
  DEL PEAK 35(19Q13.43) MUTATED     1 279
  DEL PEAK 35(19Q13.43) WILD-TYPE   2 289
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(19Q13.43) MUTATED      1  279
  DEL PEAK 35(19Q13.43) WILD-TYPE    2  289
     clus
vv    DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE
  NO                              1                               2
  YES                           279                             289
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 35(19Q13.43) MUTATED    9 14  1  2
  DEL PEAK 35(19Q13.43) WILD-TYPE  5 12  4  1
D68V6, multiclass
    clus
vv   DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE
  R0                             9                               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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(19Q13.43) MUTATED                                  0     6
  DEL PEAK 35(19Q13.43) WILD-TYPE                                3    12
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(19Q13.43) MUTATED                          18
  DEL PEAK 35(19Q13.43) WILD-TYPE                        14
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 35(19Q13.43) MUTATED                                           0
  DEL PEAK 35(19Q13.43) WILD-TYPE                                         1
                                 vv
clus                              WHITE
  DEL PEAK 35(19Q13.43) MUTATED     237
  DEL PEAK 35(19Q13.43) WILD-TYPE   238
D68V7, multiclass
                                           clus
vv                                          DEL PEAK 35(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               237
                                           clus
vv                                          DEL PEAK 35(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  12
  BLACK OR AFRICAN AMERICAN                                              14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               1
  WHITE                                                                 238
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                                 cls
clus                                0   1
  DEL PEAK 35(19Q13.43) MUTATED     7 155
  DEL PEAK 35(19Q13.43) WILD-TYPE   3 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(19Q13.43) MUTATED      7  155
  DEL PEAK 35(19Q13.43) WILD-TYPE    3  170
                        clus
vv                       DEL PEAK 35(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           155
                        clus
vv                       DEL PEAK 35(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             170
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 36(21Q22.3) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(21Q22.3) MUTATED   113 105
  DEL PEAK 36(21Q22.3) WILD-TYPE 153 185
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                           218                            338 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                           105                            185 
$`DEL PEAK 36(21Q22.3) MUTATED`
TCGA-04-1335 TCGA-04-1347 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 TCGA-04-1362 
        1.81        63.09        63.98        65.46        49.28        44.32 
TCGA-04-1365 TCGA-04-1638 TCGA-04-1644 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       76.57        55.43        48.89        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1655 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       31.86        45.37        35.57         9.99        38.43        89.33 
TCGA-09-1665 TCGA-09-1667 TCGA-09-1669 TCGA-09-1673 TCGA-09-1675 TCGA-09-2043 
       41.62        61.87        30.51         3.02        97.55         6.18 
TCGA-09-2044 TCGA-09-2049 TCGA-09-2050 TCGA-09-2051 TCGA-09-2056 TCGA-10-0926 
        6.12       112.41        71.11        63.09        12.46        25.91 
TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 TCGA-10-0931 TCGA-10-0937 TCGA-13-0727 
       81.47        18.51        33.24        32.28        15.12        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0761 TCGA-13-0766 TCGA-13-0791 TCGA-13-0792 
       17.82        55.17        34.06        21.40        38.93        36.72 
TCGA-13-0794 TCGA-13-0800 TCGA-13-0803 TCGA-13-0883 TCGA-13-0884 TCGA-13-0886 
       30.35         8.12        43.86        68.94       107.18        74.27 
TCGA-13-0887 TCGA-13-0891 TCGA-13-0904 TCGA-13-0906 TCGA-13-0911 TCGA-13-0912 
       66.67        69.01        48.33        44.94        27.72        34.06 
TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 
       29.98        21.17        14.89        13.81         4.64         6.41 
TCGA-13-1404 TCGA-13-1408 TCGA-13-1409 TCGA-13-1411 TCGA-13-1412 TCGA-13-1482 
        6.61         5.92         6.84         4.21         5.33        61.71 
TCGA-13-1484 TCGA-13-1487 TCGA-13-1488 TCGA-13-1489 TCGA-13-1491 TCGA-13-1495 
       98.04        22.39        70.82        82.88        52.44        49.25 
TCGA-13-1497 TCGA-13-1499 TCGA-13-1501 TCGA-13-1505 TCGA-13-1507 TCGA-13-1510 
       54.31        38.40        32.84         4.21         4.77         2.56 
TCGA-13-1512 TCGA-13-2057 TCGA-13-2059 TCGA-13-2061 TCGA-13-2065 TCGA-20-1682 
        3.09        14.24        12.23        10.78         8.75        27.52 
TCGA-20-1684 TCGA-20-1686 TCGA-20-1687 TCGA-23-1022 TCGA-23-1028 TCGA-23-1030 
       19.10         2.93         2.66        42.54        49.41        29.13 
TCGA-23-1031 TCGA-23-1032 TCGA-23-1113 TCGA-23-1114 TCGA-23-1116 TCGA-23-1117 
       18.90         2.24        31.20        68.68         4.57        33.30 
TCGA-23-1121 TCGA-23-2072 TCGA-23-2078 TCGA-23-2641 TCGA-24-0968 TCGA-24-0975 
        6.38        24.95        87.48         2.76        19.66        21.80 
TCGA-24-0980 TCGA-24-1105 TCGA-24-1413 TCGA-24-1418 TCGA-24-1422 TCGA-24-1425 
        7.66        47.41         6.31         7.99         0.76         5.95 
TCGA-24-1430 TCGA-24-1431 TCGA-24-1467 TCGA-24-1471 TCGA-24-1548 TCGA-24-1549 
       28.37        19.17       105.99         1.18        16.21        56.58 
TCGA-24-1553 TCGA-24-1557 TCGA-24-1563 TCGA-24-1603 TCGA-24-1845 TCGA-24-1849 
       58.09        39.88        47.70        90.15         3.81         5.79 
TCGA-24-1850 TCGA-24-1920 TCGA-24-2023 TCGA-24-2026 TCGA-24-2027 TCGA-24-2029 
        5.52         9.80        44.84        34.82       109.71        14.43 
TCGA-24-2035 TCGA-24-2267 TCGA-24-2281 TCGA-24-2288 TCGA-24-2290 TCGA-24-2298 
       28.18        47.54        44.61         0.82        36.23        53.26 
TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1321 TCGA-25-1627 TCGA-25-1630 
       37.02        34.98        36.95        33.96         0.36         7.86 
TCGA-25-1631 TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 
        0.30        56.94        60.59        35.54        51.22        14.96 
TCGA-25-1871 TCGA-25-1877 TCGA-25-2396 TCGA-29-1691 TCGA-29-1695 TCGA-29-1699 
       24.99        18.05         3.02        47.18         0.79         0.53 
TCGA-29-1702 TCGA-29-1705 TCGA-29-1761 TCGA-29-1763 TCGA-29-1769 TCGA-29-1770 
       18.67        18.25        17.00        66.81        22.98        24.36 
TCGA-29-1774 TCGA-29-1775 TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2425 
       17.33        12.36         5.36        34.62        86.17        65.00 
TCGA-29-2427 TCGA-29-2434 TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       62.47        11.47        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1866 TCGA-30-1891 TCGA-31-1950 
       15.68        48.10        44.91        36.62        30.05        18.77 
TCGA-31-1956 TCGA-36-1568 TCGA-36-1569 TCGA-36-1574 TCGA-36-1575 TCGA-36-1581 
       44.12        28.77        29.10        22.55         8.55        24.69 
TCGA-36-2530 TCGA-36-2538 TCGA-36-2544 TCGA-36-2545 TCGA-36-2547 TCGA-36-2548 
       33.01        25.08        20.98        18.31        20.52        14.17 
TCGA-36-2552 TCGA-3P-A9WA TCGA-42-2587 TCGA-57-1585 TCGA-57-1992 TCGA-57-1993 
       11.47         7.99        23.74         1.74        29.00        25.08 
TCGA-57-1994 TCGA-59-2354 TCGA-59-A5PD TCGA-61-1727 TCGA-61-1730 TCGA-61-1733 
       25.02        34.39        20.52        18.54         4.34        31.79 
TCGA-61-1734 TCGA-61-1737 TCGA-61-1740 TCGA-61-1899 TCGA-61-1900 TCGA-61-1903 
       28.47        44.84         2.43         8.42         5.79        13.02 
TCGA-61-1904 TCGA-61-1907 TCGA-61-1913 TCGA-61-1914 TCGA-61-1917 TCGA-61-1918 
        9.07        31.30        48.92        56.61        43.43        15.75 
TCGA-61-1919 TCGA-61-2000 TCGA-61-2008 TCGA-61-2016 TCGA-61-2094 TCGA-61-2113 
       38.17        14.50        30.64         1.18        71.74        22.22 
TCGA-61-2613 TCGA-WR-A838 
       31.07         8.05 

$`DEL PEAK 36(21Q22.3) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1343 TCGA-04-1346 TCGA-04-1348 TCGA-04-1349 TCGA-04-1361 TCGA-04-1364 
       11.87        65.52        48.76        21.57        32.52        33.67 
TCGA-04-1367 TCGA-04-1371 TCGA-04-1514 TCGA-04-1516 TCGA-04-1517 TCGA-04-1525 
       71.47        82.39        56.55        41.59        19.99        38.37 
TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1646 TCGA-04-1654 TCGA-09-0364 
      119.08        29.10        84.20        27.88        47.70        29.16 
TCGA-09-0365 TCGA-09-0366 TCGA-09-0367 TCGA-09-1664 TCGA-09-1666 TCGA-09-1668 
        9.47        57.76        17.98        74.93        57.60        55.36 
TCGA-09-1670 TCGA-09-1672 TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2053 
       17.98         5.85         8.55        35.15         4.54        39.75 
TCGA-09-2054 TCGA-09-2055 TCGA-10-0925 TCGA-10-0933 TCGA-10-0934 TCGA-10-0935 
       20.94        26.93        54.31        11.70         3.91        35.44 
TCGA-10-0936 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 
       35.80        19.86         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        31.10         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        32.25        31.04         8.45        28.70        19.59 
TCGA-13-0797 TCGA-13-0799 TCGA-13-0801 TCGA-13-0802 TCGA-13-0804 TCGA-13-0805 
        8.71         7.79         8.28         8.19        35.28        35.28 
TCGA-13-0807 TCGA-13-0885 TCGA-13-0888 TCGA-13-0889 TCGA-13-0890 TCGA-13-0893 
       13.61        91.40        70.39        61.84        67.99        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0905 
       57.47        56.15        57.07        19.36        47.38        47.84 
TCGA-13-0908 TCGA-13-0910 TCGA-13-0924 TCGA-13-1403 TCGA-13-1405 TCGA-13-1407 
       44.84        37.08         6.08        10.88         7.36         6.05 
TCGA-13-1410 TCGA-13-1477 TCGA-13-1481 TCGA-13-1483 TCGA-13-1485 TCGA-13-1492 
        4.70        54.64        87.06        29.42        20.68        73.55 
TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 TCGA-13-1504 TCGA-13-1506 
       38.20         4.24        37.61        13.97        16.57         4.41 
TCGA-13-1509 TCGA-13-1511 TCGA-13-2060 TCGA-13-2071 TCGA-13-A5FT TCGA-13-A5FU 
        4.18         3.91         8.61         6.28        54.77         8.42 
TCGA-20-0987 TCGA-20-0990 TCGA-20-0991 TCGA-20-0996 TCGA-20-1683 TCGA-20-1685 
       23.05        25.94        26.20        72.20        25.38        16.70 
TCGA-23-1021 TCGA-23-1023 TCGA-23-1024 TCGA-23-1026 TCGA-23-1027 TCGA-23-1029 
       47.54        40.54        15.39        26.83        31.76         8.81 
TCGA-23-1109 TCGA-23-1110 TCGA-23-1111 TCGA-23-1118 TCGA-23-1119 TCGA-23-1120 
       51.35        54.51         3.22        86.01       129.96         4.27 
TCGA-23-1122 TCGA-23-1123 TCGA-23-1124 TCGA-23-1809 TCGA-23-2077 TCGA-23-2079 
       39.09        33.47        58.13         0.53       115.89        91.66 
TCGA-23-2081 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0966 TCGA-24-0970 
       77.00        49.84         4.70         4.50         7.63        11.64 
TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 TCGA-24-1416 TCGA-24-1417 
       41.56        22.32        54.12        63.55         6.38         7.82 
TCGA-24-1419 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 TCGA-24-1427 TCGA-24-1428 
        7.86         6.25         6.02         5.36         4.83        17.39 
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-24-1474 TCGA-24-1544 TCGA-24-1545 TCGA-24-1546 
        9.11         3.45        22.22        26.96        57.40        64.27 
TCGA-24-1550 TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1556 TCGA-24-1558 
       41.06        51.91        41.39        88.50        70.62        19.53 
TCGA-24-1560 TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1604 
       44.09        45.50        25.87        10.26        17.23        88.37 
TCGA-24-1614 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1846 
       48.33        38.24         8.32         3.48         3.72         4.37 
TCGA-24-1847 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-1928 TCGA-24-1930 
       11.28        22.68        30.21        16.44        11.05        81.11 
TCGA-24-2019 TCGA-24-2020 TCGA-24-2024 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 
        4.87       152.02        58.16        53.95        18.48        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-24-2289 TCGA-24-2293 TCGA-24-2295 TCGA-24-2297 TCGA-25-1312 
       70.45        67.36        16.64        33.11        55.86         1.02 
TCGA-25-1313 TCGA-25-1314 TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 TCGA-25-1322 
       26.96        32.02        51.06         1.02        65.00         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1625 TCGA-25-1626 TCGA-25-1628 
       12.00         2.96        18.58        18.02        15.81        20.61 
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-29-1690 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
       26.99        78.90        44.71       101.79        38.53        33.70 
TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1703 TCGA-29-1707 TCGA-29-1710 
       31.20        68.32        16.90        59.67        41.98        29.23 
TCGA-29-1711 TCGA-29-1762 TCGA-29-1764 TCGA-29-1766 TCGA-29-1768 TCGA-29-1771 
       34.62        85.68        62.93        39.12        31.23        22.55 
TCGA-29-1776 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 TCGA-29-1783 TCGA-29-2428 
       11.84        12.30        14.93         8.38         7.23        45.11 
TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 TCGA-29-2436 TCGA-29-A5NZ TCGA-30-1857 
        4.90        42.25        11.84         9.76        21.04         0.26 
TCGA-30-1861 TCGA-30-1862 TCGA-30-1867 TCGA-30-1880 TCGA-30-1887 TCGA-30-1892 
       34.78         6.12         1.22        57.57        24.26        48.79 
TCGA-31-1944 TCGA-31-1946 TCGA-31-1951 TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 
       45.57        30.18        22.49         6.71        42.51         2.20 
TCGA-36-1570 TCGA-36-1571 TCGA-36-1576 TCGA-36-1577 TCGA-36-1578 TCGA-36-1580 
       21.53        22.85        30.08        25.74        27.85        24.23 
TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 TCGA-36-2537 TCGA-36-2540 TCGA-36-2542 
       35.05        29.49        29.82        25.91        23.80        21.60 
TCGA-36-2543 TCGA-36-2549 TCGA-36-2551 TCGA-42-2582 TCGA-42-2588 TCGA-42-2589 
        2.24         6.05        16.18        26.04         9.44        42.02 
TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 TCGA-57-1583 TCGA-57-1584 
        7.46        40.77         1.48        24.03        11.38        21.14 
TCGA-57-1586 TCGA-59-2348 TCGA-59-2349 TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 
       22.32       180.20        80.12        22.32       116.12         9.40 
TCGA-59-2355 TCGA-59-2363 TCGA-59-2372 TCGA-61-1721 TCGA-61-1722 TCGA-61-1724 
        2.14         5.42        44.81        11.11         8.09        20.94 
TCGA-61-1725 TCGA-61-1728 TCGA-61-1736 TCGA-61-1738 TCGA-61-1741 TCGA-61-1743 
       31.43        27.88        48.79        35.80        33.67        43.69 
TCGA-61-1895 TCGA-61-1901 TCGA-61-1906 TCGA-61-1910 TCGA-61-1911 TCGA-61-1915 
        1.45        11.41        34.13        37.05        42.51        67.76 
TCGA-61-1995 TCGA-61-1998 TCGA-61-2002 TCGA-61-2003 TCGA-61-2009 TCGA-61-2012 
        2.01         5.52        17.98         4.01        39.85        30.64 
TCGA-61-2017 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 TCGA-61-2092 TCGA-61-2095 
       45.96        45.40         4.80         4.77        51.72        61.64 
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-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2612 TCGA-61-2614 TCGA-OY-A56P 
       20.68        44.52       125.75         6.35         8.61        39.68 
TCGA-OY-A56Q TCGA-VG-A8LO 
       18.94         0.79 

  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                          0.30                           0.26 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                        112.41                         180.20 
  DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE 
                        28.420                         27.865 
[1] "0.3 - 112.4 (28.4)" "0.3 - 180.2 (27.9)"
[1] "hr=" "1.1"
D69V2, continuous
                                vv
clus                             OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 36(21Q22.3) MUTATED         1   219                0
  DEL PEAK 36(21Q22.3) WILD-TYPE       1   338                2
D69V3, multiclass
                  clus
vv                 DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE
  OMENTUM                                     1                              1
  OVARY                                     219                            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"
D69V4, continuous
D69V5, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q22.3) MUTATED     1 222
  DEL PEAK 36(21Q22.3) WILD-TYPE   2 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.3) MUTATED      1  222
  DEL PEAK 36(21Q22.3) WILD-TYPE    2  346
     clus
vv    DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE
  NO                             1                              2
  YES                          222                            346
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 36(21Q22.3) MUTATED    5 11  0  1
  DEL PEAK 36(21Q22.3) WILD-TYPE  9 15  5  2
D69V6, multiclass
    clus
vv   DEL PEAK 36(21Q22.3) MUTATED DEL PEAK 36(21Q22.3) WILD-TYPE
  R0                            5                              9
  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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(21Q22.3) MUTATED                                  0     6
  DEL PEAK 36(21Q22.3) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(21Q22.3) MUTATED                          11
  DEL PEAK 36(21Q22.3) WILD-TYPE                        21
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 36(21Q22.3) MUTATED                                           0
  DEL PEAK 36(21Q22.3) WILD-TYPE                                         1
                                vv
clus                             WHITE
  DEL PEAK 36(21Q22.3) MUTATED     188
  DEL PEAK 36(21Q22.3) WILD-TYPE   287
D69V7, multiclass
                                           clus
vv                                          DEL PEAK 36(21Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           11
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                              188
                                           clus
vv                                          DEL PEAK 36(21Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              1
  WHITE                                                                287
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q22.3) MUTATED     6 133
  DEL PEAK 36(21Q22.3) WILD-TYPE   4 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q22.3) MUTATED      6  133
  DEL PEAK 36(21Q22.3) WILD-TYPE    4  192
                        clus
vv                       DEL PEAK 36(21Q22.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK 36(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 37(22Q13.32) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 37(22Q13.32) MUTATED   232 249
  DEL PEAK 37(22Q13.32) WILD-TYPE  34  41
  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                            481                              75 
  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                            249                              41 
$`DEL PEAK 37(22Q13.32) MUTATED`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1336 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 
       40.24        41.00        49.15         2.01        46.62        18.51 
TCGA-04-1346 TCGA-04-1347 TCGA-04-1349 TCGA-04-1350 TCGA-04-1351 TCGA-04-1356 
       65.52        63.09        21.57        63.98        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        71.47        82.39 
TCGA-04-1514 TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 
       56.55        19.99        38.37       119.08        29.10        84.20 
TCGA-04-1638 TCGA-04-1644 TCGA-04-1646 TCGA-04-1648 TCGA-04-1649 TCGA-04-1651 
       55.43        48.89        27.88        28.64        64.64        36.23 
TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 TCGA-09-0364 TCGA-09-0365 TCGA-09-0366 
       31.86        47.70        45.37        29.16         9.47        57.76 
TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 TCGA-09-1664 
       17.98        35.57         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-10-0925 TCGA-10-0926 TCGA-10-0927 TCGA-10-0928 TCGA-10-0930 
       12.46        54.31        25.91        81.47        18.51        33.24 
TCGA-10-0931 TCGA-10-0933 TCGA-10-0936 TCGA-10-0937 TCGA-10-0938 TCGA-13-0714 
       32.28        11.70        35.80        15.12        19.86         6.21 
TCGA-13-0717 TCGA-13-0720 TCGA-13-0723 TCGA-13-0724 TCGA-13-0725 TCGA-13-0727 
       24.59        44.55        39.58         2.73        12.39        15.19 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0757 TCGA-13-0758 TCGA-13-0761 TCGA-13-0764 
       17.82        55.17        11.18        11.38        34.06        31.04 
TCGA-13-0766 TCGA-13-0768 TCGA-13-0791 TCGA-13-0792 TCGA-13-0793 TCGA-13-0794 
       21.40         8.45        38.93        36.72        28.70        30.35 
TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 TCGA-13-0802 
       19.59         8.71         7.79         8.12         8.28         8.19 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0884 
       43.86        35.28        35.28        13.61        68.94       107.18 
TCGA-13-0885 TCGA-13-0886 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0891 
       91.40        74.27        66.67        70.39        67.99        69.01 
TCGA-13-0897 TCGA-13-0900 TCGA-13-0901 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       57.47        57.07        19.36        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0911 TCGA-13-0912 TCGA-13-0913 
       44.94        44.84        37.08        27.72        34.06        29.98 
TCGA-13-0916 TCGA-13-0919 TCGA-13-0920 TCGA-13-0921 TCGA-13-0923 TCGA-13-0924 
       21.17        14.89        13.81         4.64         6.41         6.08 
TCGA-13-1404 TCGA-13-1407 TCGA-13-1408 TCGA-13-1409 TCGA-13-1410 TCGA-13-1411 
        6.61         6.05         5.92         6.84         4.70         4.21 
TCGA-13-1412 TCGA-13-1481 TCGA-13-1482 TCGA-13-1483 TCGA-13-1484 TCGA-13-1487 
        5.33        87.06        61.71        29.42        98.04        22.39 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1495 TCGA-13-1496 TCGA-13-1497 
       52.44        73.55        38.20        49.25         4.24        54.31 
TCGA-13-1498 TCGA-13-1499 TCGA-13-1500 TCGA-13-1501 TCGA-13-1504 TCGA-13-1505 
       37.61        38.40        13.97        32.84        16.57         4.21 
TCGA-13-1506 TCGA-13-1507 TCGA-13-1509 TCGA-13-1510 TCGA-13-1511 TCGA-13-1512 
        4.41         4.77         4.18         2.56         3.91         3.09 
TCGA-13-2057 TCGA-13-2059 TCGA-13-2060 TCGA-13-2061 TCGA-13-2065 TCGA-13-2071 
       14.24        12.23         8.61        10.78         8.75         6.28 
TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0990 TCGA-20-0991 TCGA-20-1682 TCGA-20-1683 
       54.77         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        42.54 
TCGA-23-1023 TCGA-23-1024 TCGA-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 
       40.54        15.39        31.76        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         2.24        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 
        4.57        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-24-0968 
       49.84         2.76         4.70         4.50         7.63        19.66 
TCGA-24-0970 TCGA-24-0975 TCGA-24-0979 TCGA-24-0982 TCGA-24-1103 TCGA-24-1104 
       11.64        21.80        41.56        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-24-1423 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        19.17        18.67        43.53         8.55 
TCGA-24-1464 TCGA-24-1467 TCGA-24-1470 TCGA-24-1471 TCGA-24-1474 TCGA-24-1544 
       12.46       105.99         3.45         1.18        22.22        26.96 
TCGA-24-1545 TCGA-24-1546 TCGA-24-1548 TCGA-24-1549 TCGA-24-1550 TCGA-24-1552 
       57.40        64.27        16.21        56.58        41.06        41.39 
TCGA-24-1553 TCGA-24-1555 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1560 
       58.09        88.50        70.62        39.88        19.53        44.09 
TCGA-24-1562 TCGA-24-1564 TCGA-24-1565 TCGA-24-1567 TCGA-24-1603 TCGA-24-1604 
       45.50        25.87        10.26        17.23        90.15        88.37 
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-24-1850 TCGA-24-1920 TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 
       11.28         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-24-2026 
       11.05        81.11         4.87       152.02        44.84        34.82 
TCGA-24-2027 TCGA-24-2029 TCGA-24-2030 TCGA-24-2033 TCGA-24-2036 TCGA-24-2254 
      109.71        14.43        53.95        18.48        64.01        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-24-2281 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-24-2297 TCGA-24-2298 TCGA-25-1312 TCGA-25-1314 TCGA-25-1315 TCGA-25-1316 
       55.86        53.26         1.02        32.02        51.06        37.02 
TCGA-25-1317 TCGA-25-1318 TCGA-25-1319 TCGA-25-1320 TCGA-25-1321 TCGA-25-1322 
        1.02        34.98        65.00        36.95        33.96         2.99 
TCGA-25-1323 TCGA-25-1329 TCGA-25-1623 TCGA-25-1626 TCGA-25-1628 TCGA-25-1631 
       12.00         2.96        18.58        15.81        20.61         0.30 
TCGA-25-1632 TCGA-25-1633 TCGA-25-1634 TCGA-25-1635 TCGA-25-1870 TCGA-25-1871 
       56.94        60.59        35.54        51.22        14.96        24.99 
TCGA-25-1877 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 TCGA-25-2393 
       18.05        85.05        13.02        49.05         1.02        38.04 
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-25-2408 TCGA-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1695 
       31.00        26.99        78.90       101.79        38.53         0.79 
TCGA-29-1696 TCGA-29-1697 TCGA-29-1698 TCGA-29-1701 TCGA-29-1702 TCGA-29-1703 
       33.70        31.20        68.32        16.90        18.67        59.67 
TCGA-29-1705 TCGA-29-1707 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 
       18.25        41.98        34.62        17.00        85.68        66.81 
TCGA-29-1766 TCGA-29-1768 TCGA-29-1769 TCGA-29-1774 TCGA-29-1775 TCGA-29-1776 
       39.12        31.23        22.98        17.33        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        34.62 
TCGA-29-2414 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2432 
       86.17        65.00        45.11         4.90        42.25        11.84 
TCGA-29-2434 TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1855 
       11.47        21.04        38.07        51.91        36.26         2.47 
TCGA-30-1856 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1866 TCGA-30-1867 
       15.68        48.10        44.91         6.12        36.62         1.22 
TCGA-30-1880 TCGA-30-1887 TCGA-31-1944 TCGA-31-1946 TCGA-31-1950 TCGA-31-1951 
       57.57        24.26        45.57        30.18        18.77        22.49 
TCGA-31-1953 TCGA-31-1955 TCGA-31-1959 TCGA-36-1568 TCGA-36-1569 TCGA-36-1570 
        6.71        42.51         2.20        28.77        29.10        21.53 
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-3P-A9WA TCGA-42-2582 TCGA-42-2587 
        6.05        16.18        11.47         7.99        26.04        23.74 
TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 TCGA-42-2591 TCGA-42-2593 TCGA-57-1582 
        9.44        42.02         7.46        40.77         1.48        24.03 
TCGA-57-1583 TCGA-57-1584 TCGA-57-1992 TCGA-57-1993 TCGA-57-1994 TCGA-59-2348 
       11.38        21.14        29.00        25.08        25.02       180.20 
TCGA-59-2350 TCGA-59-2351 TCGA-59-2352 TCGA-59-2354 TCGA-59-2355 TCGA-59-2363 
       22.32       116.12         9.40        34.39         2.14         5.42 
TCGA-59-2372 TCGA-61-1722 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 TCGA-61-1730 
       44.81         8.09        31.43        18.54        27.88         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-61-1743 TCGA-61-1899 TCGA-61-1900 TCGA-61-1901 TCGA-61-1903 
       33.67        43.69         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-61-2000 
       43.43        15.75        38.17         2.01         5.52        14.50 
TCGA-61-2002 TCGA-61-2003 TCGA-61-2008 TCGA-61-2009 TCGA-61-2012 TCGA-61-2016 
       17.98         4.01        30.64        39.85        30.64         1.18 
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-61-2109 TCGA-61-2110 TCGA-61-2111 TCGA-61-2113 
       55.50         6.48        20.68        44.52       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 
        8.05 

$`DEL PEAK 37(22Q13.32) WILD-TYPE`
TCGA-04-1335 TCGA-04-1343 TCGA-04-1348 TCGA-04-1516 TCGA-09-1672 TCGA-09-2055 
        1.81        11.87        48.76        41.59         5.85        26.93 
TCGA-10-0934 TCGA-10-0935 TCGA-13-0726 TCGA-13-0755 TCGA-13-0760 TCGA-13-0762 
        3.91        35.44        31.10         2.50        11.54        32.25 
TCGA-13-0889 TCGA-13-0893 TCGA-13-0899 TCGA-13-1403 TCGA-13-1405 TCGA-13-1477 
       61.84        43.36        56.15        10.88         7.36        54.64 
TCGA-13-1485 TCGA-13-1488 TCGA-13-1489 TCGA-20-0987 TCGA-20-0996 TCGA-23-1026 
       20.68        70.82        82.88        23.05        72.20        26.83 
TCGA-23-1111 TCGA-23-1121 TCGA-23-1809 TCGA-23-2079 TCGA-24-0980 TCGA-24-1463 
        3.22         6.38         0.53        91.66         7.66        72.92 
TCGA-24-1466 TCGA-24-1469 TCGA-24-1551 TCGA-24-1563 TCGA-24-1614 TCGA-24-1849 
       45.14         9.11        51.91        47.70        48.33         5.79 
TCGA-24-2024 TCGA-24-2035 TCGA-24-2038 TCGA-25-1313 TCGA-25-1625 TCGA-25-1627 
       58.16        28.18        44.52        26.96        18.02         0.36 
TCGA-25-1630 TCGA-25-2396 TCGA-29-1690 TCGA-29-1691 TCGA-29-1699 TCGA-29-1710 
        7.86         3.02        44.71        47.18         0.53        29.23 
TCGA-29-1764 TCGA-29-1770 TCGA-29-1771 TCGA-29-2427 TCGA-29-2436 TCGA-30-1857 
       62.93        24.36        22.55        62.47         9.76         0.26 
TCGA-30-1861 TCGA-30-1891 TCGA-30-1892 TCGA-31-1956 TCGA-36-1571 TCGA-36-1574 
       34.78        30.05        48.79        44.12        22.85        22.55 
TCGA-36-2529 TCGA-57-1585 TCGA-57-1586 TCGA-59-2349 TCGA-59-A5PD TCGA-61-1721 
       35.05         1.74        22.32        80.12        20.52        11.11 
TCGA-61-1724 TCGA-61-1895 TCGA-61-1904 TCGA-61-1911 TCGA-61-2017 TCGA-61-2092 
       20.94         1.45         9.07        42.51        45.96        51.72 
TCGA-61-2094 TCGA-61-2095 TCGA-61-2104 
       71.74        61.64        76.87 

  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                           0.30                            0.26 
  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                         180.20                           91.66 
  DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE 
                          27.88                           28.18 
[1] "0.3 - 180.2 (27.9)" "0.3 - 91.7 (28.2)" 
[1] "hr=" "1"  
D70V2, continuous
                                 vv
clus                              OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 37(22Q13.32) MUTATED         2   483                1
  DEL PEAK 37(22Q13.32) WILD-TYPE       0    74                1
D70V3, multiclass
                  clus
vv                 DEL PEAK 37(22Q13.32) MUTATED
  OMENTUM                                      2
  OVARY                                      483
  PERITONEUM OVARY                             1
                  clus
vv                 DEL PEAK 37(22Q13.32) WILD-TYPE
  OMENTUM                                        0
  OVARY                                         74
  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, continuous
D70V5, binary
                                 cls
clus                                0   1
  DEL PEAK 37(22Q13.32) MUTATED     3 493
  DEL PEAK 37(22Q13.32) WILD-TYPE   0  75
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(22Q13.32) MUTATED      3  493
  DEL PEAK 37(22Q13.32) WILD-TYPE    0   75
     clus
vv    DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE
  NO                              3                               0
  YES                           493                              75
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 37(22Q13.32) MUTATED   12 24  5  3
  DEL PEAK 37(22Q13.32) WILD-TYPE  2  2  0  0
D70V6, multiclass
    clus
vv   DEL PEAK 37(22Q13.32) MUTATED DEL PEAK 37(22Q13.32) WILD-TYPE
  R0                            12                               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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(22Q13.32) MUTATED                                  3    17
  DEL PEAK 37(22Q13.32) WILD-TYPE                                0     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(22Q13.32) MUTATED                          27
  DEL PEAK 37(22Q13.32) WILD-TYPE                         5
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 37(22Q13.32) MUTATED                                           1
  DEL PEAK 37(22Q13.32) WILD-TYPE                                         0
                                 vv
clus                              WHITE
  DEL PEAK 37(22Q13.32) MUTATED     409
  DEL PEAK 37(22Q13.32) WILD-TYPE    66
D70V7, multiclass
                                           clus
vv                                          DEL PEAK 37(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                               409
                                           clus
vv                                          DEL PEAK 37(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        0
  ASIAN                                                                   1
  BLACK OR AFRICAN AMERICAN                                               5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               0
  WHITE                                                                  66
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                                 cls
clus                                0   1
  DEL PEAK 37(22Q13.32) MUTATED     9 278
  DEL PEAK 37(22Q13.32) WILD-TYPE   1  47
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(22Q13.32) MUTATED      9  278
  DEL PEAK 37(22Q13.32) WILD-TYPE    1   47
                        clus
vv                       DEL PEAK 37(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           278
                        clus
vv                       DEL PEAK 37(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              47
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 38(XP21.1) MUTATION ANALYSIS
D71V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 38(XP21.1) MUTATED   165 179
  DEL PEAK 38(XP21.1) WILD-TYPE 101 111
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                          344                           212 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                          179                           111 
$`DEL PEAK 38(XP21.1) MUTATED`
TCGA-04-1335 TCGA-04-1336 TCGA-04-1346 TCGA-04-1347 TCGA-04-1351 TCGA-04-1361 
        1.81        49.15        65.52        63.09        65.46        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        71.47        82.39        56.55 
TCGA-04-1517 TCGA-04-1525 TCGA-04-1530 TCGA-04-1536 TCGA-04-1542 TCGA-04-1638 
       19.99        38.37       119.08        29.10        84.20        55.43 
TCGA-04-1644 TCGA-04-1648 TCGA-04-1651 TCGA-04-1652 TCGA-04-1654 TCGA-04-1655 
       48.89        28.64        36.23        31.86        47.70        45.37 
TCGA-09-0366 TCGA-09-0367 TCGA-09-0369 TCGA-09-1659 TCGA-09-1661 TCGA-09-1662 
       57.76        17.98        35.57         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-10-0925 TCGA-10-0926 TCGA-10-0927 
       20.94        26.93        12.46        54.31        25.91        81.47 
TCGA-10-0930 TCGA-10-0931 TCGA-10-0938 TCGA-13-0714 TCGA-13-0717 TCGA-13-0720 
       33.24        32.28        19.86         6.21        24.59        44.55 
TCGA-13-0723 TCGA-13-0725 TCGA-13-0727 TCGA-13-0755 TCGA-13-0757 TCGA-13-0758 
       39.58        12.39        15.19         2.50        11.18        11.38 
TCGA-13-0760 TCGA-13-0761 TCGA-13-0762 TCGA-13-0764 TCGA-13-0766 TCGA-13-0792 
       11.54        34.06        32.25        31.04        21.40        36.72 
TCGA-13-0794 TCGA-13-0795 TCGA-13-0797 TCGA-13-0799 TCGA-13-0800 TCGA-13-0801 
       30.35        19.59         8.71         7.79         8.12         8.28 
TCGA-13-0803 TCGA-13-0804 TCGA-13-0805 TCGA-13-0807 TCGA-13-0883 TCGA-13-0886 
       43.86        35.28        35.28        13.61        68.94        74.27 
TCGA-13-0889 TCGA-13-0891 TCGA-13-0900 TCGA-13-0903 TCGA-13-0904 TCGA-13-0905 
       61.84        69.01        57.07        47.38        48.33        47.84 
TCGA-13-0906 TCGA-13-0908 TCGA-13-0910 TCGA-13-0913 TCGA-13-0916 TCGA-13-0919 
       44.94        44.84        37.08        29.98        21.17        14.89 
TCGA-13-0921 TCGA-13-0924 TCGA-13-1404 TCGA-13-1405 TCGA-13-1407 TCGA-13-1408 
        4.64         6.08         6.61         7.36         6.05         5.92 
TCGA-13-1409 TCGA-13-1412 TCGA-13-1482 TCGA-13-1483 TCGA-13-1487 TCGA-13-1489 
        6.84         5.33        61.71        29.42        22.39        82.88 
TCGA-13-1491 TCGA-13-1492 TCGA-13-1494 TCGA-13-1496 TCGA-13-1498 TCGA-13-1500 
       52.44        73.55        38.20         4.24        37.61        13.97 
TCGA-13-1504 TCGA-13-1505 TCGA-13-1509 TCGA-13-1510 TCGA-13-1512 TCGA-13-2059 
       16.57         4.21         4.18         2.56         3.09        12.23 
TCGA-13-2060 TCGA-13-2065 TCGA-13-A5FT TCGA-13-A5FU TCGA-20-0987 TCGA-20-0991 
        8.61         8.75        54.77         8.42        23.05        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-23-1027 TCGA-23-1028 TCGA-23-1029 TCGA-23-1030 TCGA-23-1031 TCGA-23-1109 
       31.76        49.41         8.81        29.13        18.90        51.35 
TCGA-23-1111 TCGA-23-1113 TCGA-23-1119 TCGA-23-1121 TCGA-23-1123 TCGA-23-2077 
        3.22        31.20       129.96         6.38        33.47       115.89 
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-24-0979 TCGA-24-0980 TCGA-24-1103 TCGA-24-1104 TCGA-24-1105 TCGA-24-1413 
       41.56         7.66        54.12        63.55        47.41         6.31 
TCGA-24-1416 TCGA-24-1418 TCGA-24-1422 TCGA-24-1423 TCGA-24-1424 TCGA-24-1426 
        6.38         7.99         0.76         6.25         6.02         5.36 
TCGA-24-1427 TCGA-24-1428 TCGA-24-1430 TCGA-24-1431 TCGA-24-1435 TCGA-24-1436 
        4.83        17.39        28.37        19.17        43.53         8.55 
TCGA-24-1463 TCGA-24-1464 TCGA-24-1474 TCGA-24-1545 TCGA-24-1546 TCGA-24-1550 
       72.92        12.46        22.22        57.40        64.27        41.06 
TCGA-24-1551 TCGA-24-1552 TCGA-24-1555 TCGA-24-1560 TCGA-24-1562 TCGA-24-1563 
       51.91        41.39        88.50        44.09        45.50        47.70 
TCGA-24-1564 TCGA-24-1567 TCGA-24-1603 TCGA-24-1614 TCGA-24-1845 TCGA-24-1846 
       25.87        17.23        90.15        48.33         3.81         4.37 
TCGA-24-1847 TCGA-24-1849 TCGA-24-1920 TCGA-24-1928 TCGA-24-1930 TCGA-24-2023 
       11.28         5.79         9.80        11.05        81.11        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        53.95        18.48 
TCGA-24-2036 TCGA-24-2254 TCGA-24-2260 TCGA-24-2261 TCGA-24-2262 TCGA-24-2267 
       64.01        57.07        36.16         0.79         0.36        47.54 
TCGA-24-2271 TCGA-24-2280 TCGA-24-2288 TCGA-24-2289 TCGA-24-2290 TCGA-24-2297 
       31.63        70.45         0.82        67.36        36.23        55.86 
TCGA-24-2298 TCGA-25-1314 TCGA-25-1316 TCGA-25-1318 TCGA-25-1320 TCGA-25-1322 
       53.26        32.02        37.02        34.98        36.95         2.99 
TCGA-25-1329 TCGA-25-1625 TCGA-25-1631 TCGA-25-1632 TCGA-25-1634 TCGA-25-1635 
        2.96        18.02         0.30        56.94        35.54        51.22 
TCGA-25-1870 TCGA-25-1871 TCGA-25-1878 TCGA-25-2042 TCGA-25-2391 TCGA-25-2392 
       14.96        24.99        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-25-2409 TCGA-29-1688 TCGA-29-1693 TCGA-29-1694 TCGA-29-1696 
        2.96        26.99        78.90       101.79        38.53        33.70 
TCGA-29-1697 TCGA-29-1699 TCGA-29-1702 TCGA-29-1703 TCGA-29-1705 TCGA-29-1707 
       31.20         0.53        18.67        59.67        18.25        41.98 
TCGA-29-1710 TCGA-29-1711 TCGA-29-1761 TCGA-29-1762 TCGA-29-1763 TCGA-29-1764 
       29.23        34.62        17.00        85.68        66.81        62.93 
TCGA-29-1769 TCGA-29-1771 TCGA-29-1775 TCGA-29-1777 TCGA-29-1778 TCGA-29-1781 
       22.98        22.55        12.36        12.30        14.93         8.38 
TCGA-29-1784 TCGA-29-1785 TCGA-29-2414 TCGA-29-2427 TCGA-29-2432 TCGA-29-2434 
        5.36        34.62        86.17        62.47        11.84        11.47 
TCGA-29-A5NZ TCGA-30-1714 TCGA-30-1718 TCGA-30-1853 TCGA-30-1856 TCGA-30-1857 
       21.04        38.07        51.91        36.26        15.68         0.26 
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-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-36-1569 TCGA-36-1570 TCGA-36-1574 TCGA-36-1575 TCGA-36-1577 
       44.12        29.10        21.53        22.55         8.55        25.74 
TCGA-36-1578 TCGA-36-1580 TCGA-36-1581 TCGA-36-2529 TCGA-36-2532 TCGA-36-2534 
       27.85        24.23        24.69        35.05        29.49        29.82 
TCGA-36-2537 TCGA-36-2538 TCGA-36-2542 TCGA-36-2543 TCGA-36-2544 TCGA-36-2545 
       25.91        25.08        21.60         2.24        20.98        18.31 
TCGA-36-2547 TCGA-36-2549 TCGA-3P-A9WA TCGA-42-2582 TCGA-42-2593 TCGA-57-1583 
       20.52         6.05         7.99        26.04         1.48        11.38 
TCGA-57-1584 TCGA-57-1585 TCGA-57-1586 TCGA-57-1992 TCGA-57-1994 TCGA-59-2350 
       21.14         1.74        22.32        29.00        25.02        22.32 
TCGA-59-2363 TCGA-59-A5PD TCGA-61-1724 TCGA-61-1725 TCGA-61-1727 TCGA-61-1728 
        5.42        20.52        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-61-1913 TCGA-61-1914 TCGA-61-1915 TCGA-61-1919 TCGA-61-2000 TCGA-61-2002 
       48.92        56.61        67.76        38.17        14.50        17.98 
TCGA-61-2003 TCGA-61-2012 TCGA-61-2016 TCGA-61-2018 TCGA-61-2087 TCGA-61-2088 
        4.01        30.64         1.18        45.40         4.80         4.77 
TCGA-61-2096 TCGA-61-2098 TCGA-61-2101 TCGA-61-2104 TCGA-61-2110 TCGA-61-2612 
       58.39        65.52        55.50        76.87        44.52         6.35 
TCGA-61-2613 TCGA-61-2614 
       31.07         8.61 

$`DEL PEAK 38(XP21.1) WILD-TYPE`
TCGA-04-1331 TCGA-04-1332 TCGA-04-1337 TCGA-04-1338 TCGA-04-1342 TCGA-04-1343 
       40.24        41.00         2.01        46.62        18.51        11.87 
TCGA-04-1348 TCGA-04-1349 TCGA-04-1350 TCGA-04-1356 TCGA-04-1516 TCGA-04-1646 
       48.76        21.57        63.98        49.28        41.59        27.88 
TCGA-04-1649 TCGA-09-0364 TCGA-09-0365 TCGA-09-1665 TCGA-09-1668 TCGA-09-1672 
       64.64        29.16         9.47        41.62        55.36         5.85 
TCGA-09-1674 TCGA-09-2045 TCGA-09-2048 TCGA-09-2051 TCGA-10-0928 TCGA-10-0933 
        8.55        35.15         4.54        63.09        18.51        11.70 
TCGA-10-0934 TCGA-10-0935 TCGA-10-0936 TCGA-10-0937 TCGA-13-0724 TCGA-13-0726 
        3.91        35.44        35.80        15.12         2.73        31.10 
TCGA-13-0730 TCGA-13-0751 TCGA-13-0768 TCGA-13-0791 TCGA-13-0793 TCGA-13-0802 
       17.82        55.17         8.45        38.93        28.70         8.19 
TCGA-13-0884 TCGA-13-0885 TCGA-13-0887 TCGA-13-0888 TCGA-13-0890 TCGA-13-0893 
      107.18        91.40        66.67        70.39        67.99        43.36 
TCGA-13-0897 TCGA-13-0899 TCGA-13-0901 TCGA-13-0911 TCGA-13-0912 TCGA-13-0920 
       57.47        56.15        19.36        27.72        34.06        13.81 
TCGA-13-0923 TCGA-13-1403 TCGA-13-1410 TCGA-13-1411 TCGA-13-1477 TCGA-13-1481 
        6.41        10.88         4.70         4.21        54.64        87.06 
TCGA-13-1484 TCGA-13-1485 TCGA-13-1488 TCGA-13-1495 TCGA-13-1497 TCGA-13-1499 
       98.04        20.68        70.82        49.25        54.31        38.40 
TCGA-13-1501 TCGA-13-1506 TCGA-13-1507 TCGA-13-1511 TCGA-13-2057 TCGA-13-2061 
       32.84         4.41         4.77         3.91        14.24        10.78 
TCGA-13-2071 TCGA-20-0990 TCGA-20-0996 TCGA-23-1021 TCGA-23-1022 TCGA-23-1023 
        6.28        25.94        72.20        47.54        42.54        40.54 
TCGA-23-1024 TCGA-23-1026 TCGA-23-1032 TCGA-23-1110 TCGA-23-1114 TCGA-23-1116 
       15.39        26.83         2.24        54.51        68.68         4.57 
TCGA-23-1117 TCGA-23-1118 TCGA-23-1120 TCGA-23-1122 TCGA-23-1124 TCGA-23-1809 
       33.30        86.01         4.27        39.09        58.13         0.53 
TCGA-23-2072 TCGA-23-2078 TCGA-23-2084 TCGA-23-2643 TCGA-23-2645 TCGA-24-0968 
       24.95        87.48        49.84         4.70         4.50        19.66 
TCGA-24-0982 TCGA-24-1417 TCGA-24-1419 TCGA-24-1425 TCGA-24-1434 TCGA-24-1466 
       22.32         7.82         7.86         5.95        18.67        45.14 
TCGA-24-1467 TCGA-24-1469 TCGA-24-1470 TCGA-24-1471 TCGA-24-1544 TCGA-24-1548 
      105.99         9.11         3.45         1.18        26.96        16.21 
TCGA-24-1549 TCGA-24-1553 TCGA-24-1556 TCGA-24-1557 TCGA-24-1558 TCGA-24-1565 
       56.58        58.09        70.62        39.88        19.53        10.26 
TCGA-24-1604 TCGA-24-1616 TCGA-24-1842 TCGA-24-1843 TCGA-24-1844 TCGA-24-1850 
       88.37        38.24         8.32         3.48         3.72         5.52 
TCGA-24-1923 TCGA-24-1924 TCGA-24-1927 TCGA-24-2019 TCGA-24-2020 TCGA-24-2035 
       22.68        30.21        16.44         4.87       152.02        28.18 
TCGA-24-2038 TCGA-24-2281 TCGA-24-2293 TCGA-24-2295 TCGA-25-1312 TCGA-25-1313 
       44.52        44.61        16.64        33.11         1.02        26.96 
TCGA-25-1315 TCGA-25-1317 TCGA-25-1319 TCGA-25-1321 TCGA-25-1323 TCGA-25-1623 
       51.06         1.02        65.00        33.96        12.00        18.58 
TCGA-25-1626 TCGA-25-1627 TCGA-25-1628 TCGA-25-1630 TCGA-25-1633 TCGA-25-1877 
       15.81         0.36        20.61         7.86        60.59        18.05 
TCGA-25-2404 TCGA-25-2408 TCGA-29-1690 TCGA-29-1691 TCGA-29-1695 TCGA-29-1698 
       29.03        31.00        44.71        47.18         0.79        68.32 
TCGA-29-1701 TCGA-29-1766 TCGA-29-1768 TCGA-29-1770 TCGA-29-1774 TCGA-29-1776 
       16.90        39.12        31.23        24.36        17.33        11.84 
TCGA-29-1783 TCGA-29-2425 TCGA-29-2428 TCGA-29-2429 TCGA-29-2431 TCGA-29-2436 
        7.23        65.00        45.11         4.90        42.25         9.76 
TCGA-30-1855 TCGA-30-1859 TCGA-30-1860 TCGA-30-1862 TCGA-30-1892 TCGA-31-1959 
        2.47        48.10        44.91         6.12        48.79         2.20 
TCGA-36-1568 TCGA-36-1571 TCGA-36-1576 TCGA-36-2530 TCGA-36-2540 TCGA-36-2548 
       28.77        22.85        30.08        33.01        23.80        14.17 
TCGA-36-2551 TCGA-36-2552 TCGA-42-2587 TCGA-42-2588 TCGA-42-2589 TCGA-42-2590 
       16.18        11.47        23.74         9.44        42.02         7.46 
TCGA-42-2591 TCGA-57-1582 TCGA-57-1993 TCGA-59-2348 TCGA-59-2349 TCGA-59-2351 
       40.77        24.03        25.08       180.20        80.12       116.12 
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-61-1730 TCGA-61-1740 TCGA-61-1904 TCGA-61-1906 TCGA-61-1907 TCGA-61-1910 
        4.34         2.43         9.07        34.13        31.30        37.05 
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 
        0.79         8.05 

  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                         0.26                          0.36 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                       129.96                        180.20 
  DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE 
                        28.82                         26.96 
[1] "0.3 - 130.0 (28.8)" "0.4 - 180.2 (27.0)"
[1] "hr=" "1"  
D71V2, continuous
                               vv
clus                            OMENTUM OVARY PERITONEUM OVARY
  DEL PEAK 38(XP21.1) MUTATED         1   343                1
  DEL PEAK 38(XP21.1) WILD-TYPE       1   214                1
D71V3, multiclass
                  clus
vv                 DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE
  OMENTUM                                    1                             1
  OVARY                                    343                           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"
D71V4, continuous
D71V5, binary
                               cls
clus                              0   1
  DEL PEAK 38(XP21.1) MUTATED     3 349
  DEL PEAK 38(XP21.1) WILD-TYPE   0 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 38(XP21.1) MUTATED      3  349
  DEL PEAK 38(XP21.1) WILD-TYPE    0  219
     clus
vv    DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE
  NO                            3                             0
  YES                         349                           219
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 38(XP21.1) MUTATED    7 16  2  2
  DEL PEAK 38(XP21.1) WILD-TYPE  7 10  3  1
D71V6, multiclass
    clus
vv   DEL PEAK 38(XP21.1) MUTATED DEL PEAK 38(XP21.1) WILD-TYPE
  R0                           7                             7
  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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(XP21.1) MUTATED                                  2    11
  DEL PEAK 38(XP21.1) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(XP21.1) MUTATED                          22
  DEL PEAK 38(XP21.1) WILD-TYPE                        10
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 38(XP21.1) MUTATED                                           1   286
  DEL PEAK 38(XP21.1) WILD-TYPE                                         0   189
D71V7, multiclass
                                           clus
vv                                          DEL PEAK 38(XP21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              11
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                             286
                                           clus
vv                                          DEL PEAK 38(XP21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 7
  BLACK OR AFRICAN AMERICAN                                            10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                               189
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                               cls
clus                              0   1
  DEL PEAK 38(XP21.1) MUTATED     5 192
  DEL PEAK 38(XP21.1) WILD-TYPE   5 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 38(XP21.1) MUTATED      5  192
  DEL PEAK 38(XP21.1) WILD-TYPE    5  133
                        clus
vv                       DEL PEAK 38(XP21.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         192
                        clus
vv                       DEL PEAK 38(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           133
[1] 2 2
[1] FALSE
