[1] "ofn"        "-oTUCEC-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/UCEC-TP/22507145/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/22534122/transformed.cor.cli.txt"

nPatients in clinical file=548, in cluster file=539, common to both=539
[1] 101 539
[1] "AMP PEAK  1(1P35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           56                           483 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           56                           483 
[1] "AMP PEAK  2(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           73                           466 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           73                           466 
[1] "AMP PEAK  3(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          243                           296 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          243                           296 
[1] "AMP PEAK  4(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                        256                         283 
  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                        256                         283 
[1] "AMP PEAK  5(1Q42.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                          227                           312 
  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                          227                           312 
[1] "AMP PEAK  6(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                          122                           417 
  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                          122                           417 
[1] "AMP PEAK  7(2Q13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                        119                         420 
  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                        119                         420 
[1] "AMP PEAK  8(3P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                           82                           457 
  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                           82                           457 
[1] "AMP PEAK  9(3P14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                           65                           474 
  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                           65                           474 
[1] "AMP PEAK 10(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                          175                           364 
  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                          175                           364 
[1] "AMP PEAK 11(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          164                           375 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          164                           375 
[1] "AMP PEAK 12(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                           52                           487 
  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                           52                           487 
[1] "AMP PEAK 13(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                            89                            450 
  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                            89                            450 
[1] "AMP PEAK 14(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                           57                           482 
  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                           57                           482 
[1] "AMP PEAK 15(6P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                          117                           422 
  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                          117                           422 
[1] "AMP PEAK 16(6Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                           88                           451 
  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                           88                           451 
[1] "AMP PEAK 17(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                           93                           446 
  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                           93                           446 
[1] "AMP PEAK 18(8P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                           126                            413 
  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                           126                            413 
[1] "AMP PEAK 19(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                           162                            377 
  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                           162                            377 
[1] "AMP PEAK 20(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                           209                            330 
  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                           209                            330 
[1] "AMP PEAK 21(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                           215                            324 
  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                           215                            324 
[1] "AMP PEAK 22(9P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                           65                           474 
  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                           65                           474 
[1] "AMP PEAK 23(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                           39                           500 
  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                           39                           500 
[1] "AMP PEAK 24(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                           143                            396 
  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                           143                            396 
[1] "AMP PEAK 25(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                            52                            487 
  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                            52                            487 
[1] "AMP PEAK 26(11Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                            74                            465 
  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                            74                            465 
[1] "AMP PEAK 27(11Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                            60                            479 
  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                            60                            479 
[1] "AMP PEAK 28(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                            92                            447 
  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                            92                            447 
[1] "AMP PEAK 29(12Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                             87                             452 
  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                             87                             452 
[1] "AMP PEAK 30(12Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                           100                            439 
  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                           100                            439 
[1] "AMP PEAK 31(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                          58                          481 
  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                          58                          481 
[1] "AMP PEAK 32(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                            64                            475 
  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                            64                            475 
[1] "AMP PEAK 33(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                             79                             460 
  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                             79                             460 
[1] "AMP PEAK 34(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                            38                            501 
  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                            38                            501 
[1] "AMP PEAK 35(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                            66                            473 
  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                            66                            473 
[1] "AMP PEAK 36(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                            71                            468 
  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                            71                            468 
[1] "AMP PEAK 37(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                          75                          464 
  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                          75                          464 
[1] "AMP PEAK 38(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                           105                            434 
  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                           105                            434 
[1] "AMP PEAK 39(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                             96                             443 
  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                             96                             443 
[1] "AMP PEAK 40(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                            69                            470 
  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                            69                            470 
[1] "AMP PEAK 41(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                            92                            447 
  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                            92                            447 
[1] "AMP PEAK 42(19P13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                             99                             440 
  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                             99                             440 
[1] "AMP PEAK 43(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                         121                          418 
  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                         121                          418 
[1] "AMP PEAK 44(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                         117                          422 
  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                         117                          422 
[1] "AMP PEAK 45(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                            152                             387 
  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                            152                             387 
[1] "AMP PEAK 46(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                            152                             387 
  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                            152                             387 
[1] "AMP PEAK 47(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                            153                             386 
  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                            153                             386 
[1] "AMP PEAK 48(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                            62                            477 
  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                            62                            477 
[1] "AMP PEAK 49(XP11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                            90                            449 
  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                            90                            449 
[1] "AMP PEAK 50(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                         93                         446 
  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                         93                         446 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            71                            468 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            71                            468 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            83                            456 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            83                            456 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           26                           513 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           26                           513 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           49                           490 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           49                           490 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           52                           487 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           52                           487 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           79                           460 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           79                           460 
[1] "DEL PEAK  7(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            43                            496 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            43                            496 
[1] "DEL PEAK  8(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           94                           445 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           94                           445 
[1] "DEL PEAK  9(4P15.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                            99                            440 
  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                            99                            440 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          106                           433 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          106                           433 
[1] "DEL PEAK 11(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          130                           409 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          130                           409 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          111                           428 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          111                           428 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         46                         493 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         46                         493 
[1] "DEL PEAK 14(7P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           72                           467 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           72                           467 
[1] "DEL PEAK 15(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            41                            498 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            41                            498 
[1] "DEL PEAK 16(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           55                           484 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           55                           484 
[1] "DEL PEAK 17(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           63                           476 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           63                           476 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          119                           420 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          119                           420 
[1] "DEL PEAK 19(8P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          117                           422 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          117                           422 
[1] "DEL PEAK 20(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         80                         459 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         80                         459 
[1] "DEL PEAK 21(9Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          129                           410 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          129                           410 
[1] "DEL PEAK 22(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          132                           407 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          132                           407 
[1] "DEL PEAK 23(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            50                            489 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            50                            489 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             78                             461 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             78                             461 
[1] "DEL PEAK 25(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                           104                            435 
  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                           104                            435 
[1] "DEL PEAK 26(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                            69                            470 
  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                            69                            470 
[1] "DEL PEAK 27(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                          94                          445 
  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                          94                          445 
[1] "DEL PEAK 28(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                            56                            483 
  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                            56                            483 
[1] "DEL PEAK 29(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                             66                             473 
  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                             66                             473 
[1] "DEL PEAK 30(13Q11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                          98                          441 
  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                          98                          441 
[1] "DEL PEAK 31(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                           106                            433 
  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                           106                            433 
[1] "DEL PEAK 32(14Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                            73                            466 
  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                            73                            466 
[1] "DEL PEAK 33(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                           140                            399 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                           140                            399 
[1] "DEL PEAK 34(15Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                         115                          424 
  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                         115                          424 
[1] "DEL PEAK 35(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            92                            447 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            92                            447 
[1] "DEL PEAK 36(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                         154                          385 
  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                         154                          385 
[1] "DEL PEAK 37(16Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                           158                            381 
  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                           158                            381 
[1] "DEL PEAK 38(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           166                            373 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           166                            373 
[1] "DEL PEAK 39(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           122                            417 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           122                            417 
[1] "DEL PEAK 40(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           128                            411 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           128                            411 
[1] "DEL PEAK 41(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           105                            434 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           105                            434 
[1] "DEL PEAK 42(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                            114                             425 
  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                            114                             425 
[1] "DEL PEAK 43(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                            90                            449 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                            90                            449 
[1] "DEL PEAK 44(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                          98                          441 
  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                          98                          441 
[1] "DEL PEAK 45(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           157                            382 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           157                            382 
[1] "DEL PEAK 46(19P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                          58                          481 
  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                          58                          481 
[1] "DEL PEAK 47(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                             67                             472 
  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                             67                             472 
[1] "DEL PEAK 48(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                            35                            504 
  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                            35                            504 
[1] "DEL PEAK 49(22Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                            95                            444 
  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                            95                            444 
[1] "DEL PEAK 50(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                            140                             399 
  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                            140                             399 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           88                           451 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           88                           451 
[1] "data2feature, selection=ALL"
 [1] "VITAL_STATUS"                        
 [2] "DAYS_TO_DEATH"                       
 [3] "DAYS_TO_LAST_FOLLOWUP"               
 [4] "TUMOR_TISSUE_SITE"                   
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[10] "DAYS_TO_LAST_KNOWN_ALIVE"            
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RESIDUAL_TUMOR"                      

Input Data has 13 rows and 539 columns.

[1] "Last Follow UP"
Variable 1:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 2:'DAYS_TO_DEATH':	nDistinctValues=88,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 3:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=411,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 4:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ENDOMETRIAL OTHER  SPECIFY
freq.values   "538"       "1"           
freq.contrast "1"         "538"         
both >= 3     "FALSE"     "FALSE"       
Variable 5:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 10:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 539 columns, 1 survival variables, and 3 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RESIDUAL_TUMOR"   
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P35.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P35.2) MUTATED    42  14
  AMP PEAK  1(1P35.2) WILD-TYPE 405  76
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           56                           481 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           14                            76 
$`AMP PEAK  1(1P35.2) MUTATED`
TCGA-2E-A9G8 TCGA-AP-A05D TCGA-AX-A2HF TCGA-B5-A0JN TCGA-D1-A3JP TCGA-KP-A3VZ 
       41.06        57.80        27.88        80.38        16.93        23.74 
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-AJ-A3BF 
       37.02        65.75        37.91        31.99       118.19        18.12 
TCGA-AJ-A3EJ TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A3K1 
        1.64        63.91        45.53        48.79        97.71        21.90 
TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1CF TCGA-AX-A2H5 TCGA-AX-A3G1 TCGA-AX-A3G4 
       36.13        37.78        76.83        71.24        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A1MS TCGA-B5-A3S1 
        0.26         0.30        27.29        27.85       102.31        29.65 
TCGA-BG-A18C TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N 
       15.45        16.64        92.88        22.55        11.51        31.07 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NX TCGA-D1-A3JQ TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       14.73        28.08        18.25        17.29        49.15        37.71 
TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A3L3 
       19.40        22.26        16.34        23.90        11.08        27.35 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-KP-A3W1 
       68.38        77.33        96.69        59.01        59.28         9.47 
TCGA-PG-A5BC TCGA-SL-A6J9 
       23.24         0.07 

$`AMP PEAK  1(1P35.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0KB 
       12.26        36.39        23.05        61.18         1.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       22.06        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       22.78        17.88        10.19        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
        0.43        39.52        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 
       42.35        15.95        31.99        36.33        33.07        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       18.41        20.25        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        34.16        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
      129.80        21.99        23.31        86.07        48.03        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        60.23        45.86        27.85        51.12         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       32.02        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58         4.77        30.12        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       93.50        71.84        39.35        27.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22         0.72        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
       15.88         4.27        18.84         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
       45.57        16.04         7.36        16.80        10.92        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        29.10        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EX 
       14.70        16.96        39.88         7.99        25.22         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        30.67        41.56        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 
       14.04        13.28        26.10        18.21        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                       118.19                        225.50 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                        27.98                         30.02 
[1] "0.1 - 118.2 (28.0)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.6"
D1V2, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P35.2) MUTATED    28  23
  AMP PEAK  1(1P35.2) WILD-TYPE 262 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P35.2) MUTATED     28   23
  AMP PEAK  1(1P35.2) WILD-TYPE  262  201
     clus
vv    AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE
  NO                           28                           262
  YES                          23                           201
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  1(1P35.2) MUTATED                                        15
  AMP PEAK  1(1P35.2) WILD-TYPE                                     389
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  1(1P35.2) MUTATED                               5
  AMP PEAK  1(1P35.2) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  1(1P35.2) MUTATED                                  36
  AMP PEAK  1(1P35.2) WILD-TYPE                                77
D1V3, multiclass
                                         clus
vv                                        AMP PEAK  1(1P35.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          15
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                36
                                         clus
vv                                        AMP PEAK  1(1P35.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           389
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P35.2) MUTATED    35   2   3   7
  AMP PEAK  1(1P35.2) WILD-TYPE 336  20  13  33
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE
  R0                          35                           336
  R1                           2                            20
  R2                           3                            13
  RX                           7                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1P34.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1P34.2) MUTATED    51  22
  AMP PEAK  2(1P34.2) WILD-TYPE 396  68
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           73                           464 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           22                            68 
$`AMP PEAK  2(1P34.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A3G3 
       41.06        10.19        67.66        36.39        23.05         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-EY-A212 TCGA-EY-A214 TCGA-A5-A0G5 TCGA-A5-A0GJ 
       80.38        27.09        10.19        14.40        37.02        65.75 
TCGA-A5-A1OG TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3TW 
       31.99        14.96        20.25        14.43        34.16        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 
       20.78        21.99        45.53        48.79       125.42        21.90 
TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A2H4 
       36.13        35.74        37.78        34.65        76.83        30.12 
TCGA-AX-A2H5 TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-B5-A11I TCGA-B5-A3S1 
       71.24        20.52         0.30         0.26        75.72        29.65 
TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16I 
       34.13        15.45        16.64        92.88        22.55        11.51 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A2G7 TCGA-D1-A3JQ TCGA-DI-A1NO TCGA-EO-A1Y7 
       31.07        14.73        58.95        17.29         9.37        49.15 
TCGA-EO-A1Y8 TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GV 
       37.71        34.39        22.26        16.34        23.90        15.81 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2CY 
       11.08        12.59        20.05        29.10        11.38        68.38 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
       77.33        96.69        59.01         9.34        30.67        59.28 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK  2(1P34.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D 
       20.81       110.63        57.80        93.99        95.47        12.26 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       61.18        27.88        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 
       16.93        33.30         6.21        22.78        17.88        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      149.56        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      123.68        74.10        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK 
       34.95        25.51        11.21        18.41        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       16.87        22.32        12.82         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
      129.80        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.62        20.91       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        60.23        45.86        27.85        51.12         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        32.91        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       34.09        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.20         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       93.50        71.84        39.35        27.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       14.83        13.78        14.73        14.01        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
       15.88         4.27        18.84         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        10.92        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       18.84        17.62        22.03        16.11        32.78        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       19.33        22.82        45.76        31.04        27.35        32.52 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        14.70        16.96        39.88         7.99        25.22 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A5BC TCGA-PG-A6IB 
       28.93        41.56        78.38         1.74        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       125.42                        225.50 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                        23.90                         30.15 
[1] "0.1 - 125.4 (23.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.4"
D2V2, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    38  31
  AMP PEAK  2(1P34.2) WILD-TYPE 252 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     38   31
  AMP PEAK  2(1P34.2) WILD-TYPE  252  193
     clus
vv    AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  NO                           38                           252
  YES                          31                           193
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  2(1P34.2) MUTATED                                        21
  AMP PEAK  2(1P34.2) WILD-TYPE                                     383
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  2(1P34.2) MUTATED                               7
  AMP PEAK  2(1P34.2) WILD-TYPE                            15
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  2(1P34.2) MUTATED                                  45
  AMP PEAK  2(1P34.2) WILD-TYPE                                68
D2V3, multiclass
                                         clus
vv                                        AMP PEAK  2(1P34.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          21
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                45
                                         clus
vv                                        AMP PEAK  2(1P34.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           383
  MIXED SEROUS AND ENDOMETRIOID                                      15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P34.2) MUTATED    45   4   5   7
  AMP PEAK  2(1P34.2) WILD-TYPE 326  18  11  33
D2V4, multiclass
    clus
vv   AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  R0                          45                           326
  R1                           4                            18
  R2                           5                            11
  RX                           7                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(1Q21.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1Q21.3) MUTATED   191  51
  AMP PEAK  3(1Q21.3) WILD-TYPE 256  39
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                          242                           295 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                           51                            39 
$`AMP PEAK  3(1Q21.3) MUTATED`
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH 
       88.18        30.15        16.83        29.39        20.81        10.19 
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN 
      110.63        93.99        23.05        61.18         1.38        80.38 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 
       22.06        61.87        51.55         1.81         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A549 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       19.89        73.32        36.00        23.74         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GG TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A1OG 
      123.68        60.53        36.82        28.27        54.02        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N 
       33.07        66.15        14.96        11.21        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       10.26        34.16        18.12        18.90         1.64        22.26 
TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       36.99        21.21        15.62        14.76        16.87        16.87 
TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A 
       20.78         0.13       129.80        21.99        23.31        63.91 
TCGA-AP-A05H TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       45.53        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LO TCGA-AP-A1DM 
      110.37        36.36        97.71        83.97        33.40        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       31.30        35.54        45.86        51.12        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
       13.58        80.55        88.24        71.51        35.34        79.46 
TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C8 TCGA-AX-A1CA 
       49.87        61.08        37.78        77.39        25.51        32.02 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H5 
       76.83        85.48        73.41        80.25         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3G1 TCGA-AX-A3G4 
       40.80        81.37        17.75        31.13        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT 
        0.26         1.18        14.47         0.39        56.91        55.30 
TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       86.01        48.59        57.76        64.21        63.55        13.45 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z 
       75.72        52.04        32.09        77.23        73.28        17.36 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FH TCGA-B5-A3S1 
      102.31        11.87        52.54        31.36        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        34.13        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       71.24        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A3EW 
       51.06        52.83        13.78        15.45         9.57        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0VI 
       16.64        61.87        30.74        92.88        72.72        86.99 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I 
       16.83         8.55         0.56         3.68         0.66        11.51 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       18.67         3.95        30.15        18.02         1.58         7.00 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A2G6 
       26.37        10.22        11.15        18.02         2.07         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS 
       58.95        15.88        18.84        17.29        71.61       109.08 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
       27.16        16.31         9.37        12.39       110.10        79.10 
TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS 
       45.57         7.36        10.92        37.71        51.52        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GD 
       27.16        26.96        22.26        16.34        54.15        53.88 
TCGA-EY-A1GF TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       27.16        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OO 
       32.78        15.81        37.05        12.59        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        29.10        27.35        11.38        14.70        16.96 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       77.33        59.01         9.34        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       78.38         1.74        14.04        13.28         9.47        26.10 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A917 TCGA-QS-A744 TCGA-QS-A8F1 
       38.70        22.59         8.19         6.97        14.83         4.44 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

$`AMP PEAK  3(1Q21.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GM TCGA-AJ-A3BG TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       41.06        60.53        18.08        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0YV 
       12.26        36.39        27.88        27.09        66.41        12.56 
TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A72D 
       14.27        19.79        16.93        18.87        17.92         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-A5-A0G1 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       66.77        13.84       106.88       112.54       105.37        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       65.75        46.55        73.87        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       31.99        36.33       118.19        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       25.51        18.41        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3OJ 
       33.90        14.66        22.49        17.06        20.65        15.35 
TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A056 
       15.95        22.32        12.82         2.70        35.11        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM 
       48.03        36.89        23.87        66.25        46.72        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 
       90.97        46.78        49.15         6.71        60.23        27.85 
TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06F TCGA-AX-A06H 
        0.56        33.21        29.69        45.99        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
       30.02        60.66        35.74        43.82        40.11        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN 
       32.91        34.65        26.37        25.91        34.09        37.58 
TCGA-AX-A2H4 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       30.12        34.32        46.49        38.24        30.74         2.96 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY 
        0.30        18.35        86.37        59.24        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11E 
       71.44        36.49        72.62        27.29        27.85        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 
       85.78        16.73        19.56        19.50        18.41        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A3F9 
      225.50        50.89        51.45        14.70        48.43       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0LW 
       96.30        93.50        71.84        39.35        34.95        18.61 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       43.30        52.01        34.29        52.64        56.58        14.83 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.73        14.01        15.45        20.02        23.70        20.12 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       22.39        34.98        35.90        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       67.99        96.49        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       81.57        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       66.48        29.95         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A179 TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
       14.73         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22         0.72        18.25        16.87        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV 
        3.95        48.79         4.27         2.20       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2L0 TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       10.92        25.91        39.29        36.62        24.30        35.38 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G 
       31.10        23.38        58.95         2.37        16.04        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        19.40        50.73        35.15        38.07        46.42 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI 
       38.47        51.09        14.99        24.36        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A2OM 
       23.90        33.34        32.71        11.08        19.33        22.82 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       32.52        14.14        68.38        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-JU-AAVI TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       96.69        59.28        17.75        18.21        23.24        21.30 
TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI 
       17.16        22.65        39.95        24.95        23.64        20.75 
TCGA-SJ-A6ZJ 
       18.28 

  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                       149.56                        225.50 
  AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE 
                        27.50                         30.74 
[1] "0.1 - 149.6 (27.5)" "0.2 - 225.5 (30.7)"
[1] "hr=" "1.7"
D3V2, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q21.3) MUTATED   127 103
  AMP PEAK  3(1Q21.3) WILD-TYPE 163 121
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q21.3) MUTATED    127  103
  AMP PEAK  3(1Q21.3) WILD-TYPE  163  121
     clus
vv    AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  NO                          127                           163
  YES                         103                           121
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                                       159
  AMP PEAK  3(1Q21.3) WILD-TYPE                                     245
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  3(1Q21.3) MUTATED                              10
  AMP PEAK  3(1Q21.3) WILD-TYPE                            12
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  3(1Q21.3) MUTATED                                  74
  AMP PEAK  3(1Q21.3) WILD-TYPE                                39
D3V3, multiclass
                                         clus
vv                                        AMP PEAK  3(1Q21.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         159
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                74
                                         clus
vv                                        AMP PEAK  3(1Q21.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           245
  MIXED SEROUS AND ENDOMETRIOID                                      12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1Q21.3) MUTATED   167   9  10  18
  AMP PEAK  3(1Q21.3) WILD-TYPE 204  13   6  22
D3V4, multiclass
    clus
vv   AMP PEAK  3(1Q21.3) MUTATED AMP PEAK  3(1Q21.3) WILD-TYPE
  R0                         167                           204
  R1                           9                            13
  R2                          10                             6
  RX                          18                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(1Q22) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(1Q22) MUTATED   200  56
  AMP PEAK  4(1Q22) WILD-TYPE 247  34
  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                        256                         281 
  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                         56                          34 
$`AMP PEAK  4(1Q22) MUTATED`
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH 
       88.18        30.15        16.83        29.39        20.81        10.19 
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
      110.63        93.99        23.05        27.88         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A221 
       27.09        22.06        61.87        51.55        12.56         1.81 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A549 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       10.19        14.40        19.89        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
        0.43        39.52        10.29       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU 
       17.85        32.78       123.68        60.53        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 
       54.02        31.99        36.33        33.07        66.15        28.64 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NC 
       34.16        18.12        18.90         1.64        22.26        36.99 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       21.21        15.62        14.76        16.87        16.87        20.78 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H 
        0.13       129.80        21.99        23.31        63.91        45.53 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LH 
       12.62        20.91        48.79       117.99       110.37        36.36 
TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LO TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       97.71        83.97        33.40        55.89        31.30        35.54 
TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05W 
       45.86        51.12        21.90        36.13        13.58        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS 
       88.24        71.51        35.34        79.46        49.87        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       35.74        37.78        77.39        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H4 
       32.02        76.83        85.48        73.41        80.25        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A2IO 
       71.24        40.80        81.37        17.75        31.13        64.93 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GB 
       43.82        20.52         0.30         0.26         1.18        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K3 
        0.39        56.91        55.30        86.01        48.59        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11P TCGA-B5-A11Q 
       57.76        64.21        63.55        13.45        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
       77.23        73.28        17.36       102.31        50.89        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       52.54        31.36        27.65        29.65        41.06        34.13 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0MO 
       20.19        19.33        20.94        35.21        71.24        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0W1 
       59.74        21.17        20.28        15.42        51.06        52.83 
TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CC 
       13.78        15.45         9.57        11.31        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI 
       31.00        31.76        24.99        24.13        16.64        61.87 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0VI TCGA-D1-A0ZN 
       30.74        97.41        92.88        72.72        86.99        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16O 
        8.55         0.56         3.68         0.66        11.51        33.63 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       18.67         3.95        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NX 
        7.00        28.08        26.37        10.22        11.15        18.25 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       18.02         2.07         8.48        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1NO 
       17.29        71.61       109.08        27.16        16.31         9.37 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EO-A1Y5 
       12.39       110.10        79.10        45.57         7.36        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       37.71        51.52        34.39        27.16        26.96        22.26 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       54.15        53.88        27.16        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A210 
       22.03        16.11        32.78        15.81        37.05        12.59 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       20.05        45.76        31.04        29.10        27.35        11.38 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       14.70        16.96        77.33        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 
       13.28         9.47        26.10        38.70        22.59         6.97 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44         0.07         0.23 

$`AMP PEAK  4(1Q22) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GM TCGA-AJ-A3BG TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       41.06        60.53        18.08        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-BG-A0M8 TCGA-BG-A220 TCGA-D1-A0ZO 
       12.26        36.39        61.18        66.41        14.27        19.79 
TCGA-D1-A3JP TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       16.93        18.87        17.92         5.88        66.77        13.84 
TCGA-A5-A0G1 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP 
      106.88       112.54       105.37        74.10        65.75        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       73.87        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K2 
       24.62        29.06        42.35        15.95        31.99       118.19 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       24.72        34.95        25.51        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE 
       34.36        33.90        14.66        22.49        17.06        20.65 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       15.35        15.95        22.32        12.82         2.70        35.11 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L9 TCGA-AP-A0LG 
       86.07        48.03        36.89        23.87       125.42        66.25 
TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       46.72        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       25.08        71.67        90.97        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 
       60.23        27.85         0.56        33.21        29.69        45.99 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IZ TCGA-AX-A0J0 
       57.47        27.39        30.02        60.66        43.82        40.11 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN TCGA-AX-A2H2 
       13.28        32.91        25.91        34.09        37.58         4.77 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A3FS 
       34.32        46.49        38.24        30.74         2.96         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JS 
        0.20         0.56         0.20         0.30        18.35        86.37 
TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 
       59.24        58.75        69.27        71.44        36.49        72.62 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A11V 
       54.44        73.64        61.68        85.78        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW 
       19.50        18.41        16.57       225.50        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       48.43       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.95        18.61        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       48.56        23.47        43.30        52.01        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A2AD 
       56.58        14.83        14.73        14.01        15.45        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A56F 
       23.70        20.12        22.39        34.98        35.90        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0UA TCGA-BS-A0UF 
        4.80        77.95        67.99        96.49       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       83.64        66.48        29.95         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        1.91        29.33        32.58        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        29.92        31.07 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17N TCGA-D1-A17Q 
        0.99        30.44         1.28        28.01         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NY TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 
       16.87        15.06         1.05         3.95        48.79        58.95 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2L0 TCGA-DI-A1BU 
        2.20       100.83        89.33        10.92        25.91        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        35.38        31.10        23.38        58.95 
TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        2.37        16.04        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       66.90        46.26        57.60        51.42        19.40        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        38.07        46.42        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       14.99        24.36        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A3QX TCGA-EY-A548 
       32.71        11.08        19.33        22.82        32.52        14.14 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-JU-AAVI 
       68.38        39.88         7.99        25.22        96.69        17.75 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-QF-A5YS 
       18.21        23.24        21.30         8.19        17.16        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        20.75        18.28 

  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                       0.07                        0.20 
  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                     149.56                      225.50 
  AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE 
                      27.98                       31.10 
[1] "0.1 - 149.6 (28.0)" "0.2 - 225.5 (31.1)"
[1] "hr=" "2"  
D4V2, binary
                             cls
clus                            0   1
  AMP PEAK  4(1Q22) MUTATED   137 107
  AMP PEAK  4(1Q22) WILD-TYPE 153 117
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(1Q22) MUTATED    137  107
  AMP PEAK  4(1Q22) WILD-TYPE  153  117
     clus
vv    AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE
  NO                        137                         153
  YES                       107                         117
[1] 2 2
[1] FALSE
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  4(1Q22) MUTATED                                       165
  AMP PEAK  4(1Q22) WILD-TYPE                                     239
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  4(1Q22) MUTATED                              11
  AMP PEAK  4(1Q22) WILD-TYPE                            11
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  4(1Q22) MUTATED                                  80
  AMP PEAK  4(1Q22) WILD-TYPE                                33
D4V3, multiclass
                                         clus
vv                                        AMP PEAK  4(1Q22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                       165
  MIXED SEROUS AND ENDOMETRIOID                                  11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              80
                                         clus
vv                                        AMP PEAK  4(1Q22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         239
  MIXED SEROUS AND ENDOMETRIOID                                    11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  4(1Q22) MUTATED   174  11  11  18
  AMP PEAK  4(1Q22) WILD-TYPE 197  11   5  22
D4V4, multiclass
    clus
vv   AMP PEAK  4(1Q22) MUTATED AMP PEAK  4(1Q22) WILD-TYPE
  R0                       174                         197
  R1                        11                          11
  R2                        11                           5
  RX                        18                          22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(1Q42.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(1Q42.3) MUTATED   181  45
  AMP PEAK  5(1Q42.3) WILD-TYPE 266  45
  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                          226                           311 
  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                           45                            45 
$`AMP PEAK  5(1Q42.3) MUTATED`
TCGA-A5-A0GI TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF 
       88.18        30.15        16.83        20.81        10.19        93.99 
TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       67.66        23.05         1.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       61.87        51.55         1.81         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A549 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       19.89        73.32        36.00         0.43        39.52        10.29 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GJ 
      149.56        83.51        17.85        32.78       123.68        65.75 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A1OG 
       60.53        36.82        28.27        54.02        68.65        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-A5-A7WJ 
       36.33        33.07        66.15        28.64        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NC 
       18.41        10.26        18.90         1.64        22.26        36.99 
TCGA-AJ-A3NF TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A051 
       21.21        14.76        16.87        16.87         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       21.99        23.31        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LO TCGA-AP-A1DM 
      110.37        36.36        97.71        83.97        33.40        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 
       31.30        35.54        46.78        45.86        51.12        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       36.13         0.56        13.58        88.24        71.51        35.34 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       79.46        49.87        61.08        35.74        37.78        77.39 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       25.51        26.37        32.02        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2HK 
       80.25         4.77        40.80        81.37        17.75         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       31.13        64.93         0.56        43.82        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT 
        0.26         1.18        14.47         0.39        56.91        55.30 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       86.01        58.75        48.59        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       13.45        59.84        75.72        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MU TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FH 
       73.28        17.36        50.89        52.54        31.36        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       29.65        41.06        34.95        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       35.21        71.24        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A222 TCGA-BG-A3EW 
       15.42        51.06        52.83        13.78         9.57        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        31.76        24.99        24.13 
TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0VI 
       61.87        30.74        92.88        72.72        59.51        86.99 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I 
       16.83         8.55         0.56         3.68         0.66        11.51 
TCGA-D1-A16S TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
       18.67        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A1NZ 
       28.08        26.37        10.22        11.15        16.87        18.02 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2KZ 
        8.48        15.88        18.84        17.29       109.08        27.16 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A22Y 
       16.31        35.38        45.57         7.36        10.92        51.52 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF TCGA-EY-A1GO 
       34.39        27.16        54.15        53.88        27.16        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       18.84        17.62        22.03        16.11        32.78        37.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 
       45.76        31.04        11.38        14.70        16.96        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       59.01         9.34        41.56        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 
       14.04        13.28        26.10        38.70        22.59         6.97 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44         0.07         0.23 

$`AMP PEAK  5(1Q42.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GM TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D 
       41.06        60.53        29.39        18.08       110.63        57.80 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       95.47        12.26        36.39        61.18        27.88        80.38 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A72D 
       12.56        14.27        19.79        18.87        17.92         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-KP-A3VZ TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0GD 
       66.77        13.84        23.74       106.88        37.02       112.54 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0R6 
      105.37        74.10        46.55        73.87        23.21        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       31.99       118.19        24.72        34.95        25.51        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       14.43        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE 
       18.12        33.90        14.66        22.49        17.06        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.62        15.35        15.95        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        2.70        35.11        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM 
       36.89        23.87        12.62        66.25        46.72        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AX-A05T 
       90.97        49.15         6.71        60.23        27.85        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A062 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       29.69        80.55        45.99        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       60.66        43.82        40.11        13.28        32.91        34.65 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HC 
       25.91        34.09        37.58        30.12        71.24        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       46.49        38.24        30.74         0.23         0.20         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JY TCGA-B5-A0JZ 
        0.30        18.35        86.37        59.24        69.27        71.44 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G 
       36.49        72.62        27.29        27.85       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11U 
       88.34        54.44        73.64        61.68        85.78        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.56        19.50        18.41        16.57       225.50       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FA 
       51.45        14.70        48.43        11.87       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0M7 
       93.50        71.84        39.35        34.13        18.61        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 
       52.01        34.29        52.64        56.58        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45        15.45        20.02        23.70        20.12 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       22.39        34.98        35.90        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       77.95        67.99        96.49        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       82.39        81.57        73.25        89.59        63.58        83.64 
TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       66.48        29.95         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17N 
        6.64         0.99        30.44         1.28        28.01         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
        1.78        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        0.72        18.25         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
       48.79        58.95         4.27         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2L0 TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       89.33        10.92        25.91        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10       110.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       58.95         2.37        16.04        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       19.40        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GE 
       22.26        16.34        38.47        51.09        14.99        24.36 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GV 
       23.34        23.34        23.90        33.34        32.71        15.81 
TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       11.08        19.33        12.59        22.82        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       27.35        32.52        14.14        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-KP-A3W1 
       25.22        96.69        28.93        30.67        59.28         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-QF-A5YS 
       18.21        23.24        21.30         8.19        17.16        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        20.75        18.28 

  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                       149.56                        225.50 
  AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE 
                        29.90                         29.92 
[1] "0.1 - 149.6 (29.9)" "0.2 - 225.5 (29.9)"
[1] "hr=" "1.4"
D5V2, binary
                               cls
clus                              0   1
  AMP PEAK  5(1Q42.3) MUTATED   127  88
  AMP PEAK  5(1Q42.3) WILD-TYPE 163 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(1Q42.3) MUTATED    127   88
  AMP PEAK  5(1Q42.3) WILD-TYPE  163  136
     clus
vv    AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE
  NO                          127                           163
  YES                          88                           136
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  5(1Q42.3) MUTATED                                       162
  AMP PEAK  5(1Q42.3) WILD-TYPE                                     242
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  5(1Q42.3) MUTATED                               8
  AMP PEAK  5(1Q42.3) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  5(1Q42.3) MUTATED                                  57
  AMP PEAK  5(1Q42.3) WILD-TYPE                                56
D5V3, multiclass
                                         clus
vv                                        AMP PEAK  5(1Q42.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         162
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                57
                                         clus
vv                                        AMP PEAK  5(1Q42.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           242
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(1Q42.3) MUTATED   156  10   7  12
  AMP PEAK  5(1Q42.3) WILD-TYPE 215  12   9  28
D5V4, multiclass
    clus
vv   AMP PEAK  5(1Q42.3) MUTATED AMP PEAK  5(1Q42.3) WILD-TYPE
  R0                         156                           215
  R1                          10                            12
  R2                           7                             9
  RX                          12                            28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(2P24.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(2P24.3) MUTATED    85  36
  AMP PEAK  6(2P24.3) WILD-TYPE 362  54
  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                          121                           416 
  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                           36                            54 
$`AMP PEAK  6(2P24.3) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 
       29.39        18.08        10.19        23.05        27.88         1.38 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-E6-A8L9 
       22.06        66.41        51.55        19.79        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-A5-A0G2 
        6.21        10.19        14.40         5.88        23.74       149.56 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R6 TCGA-A5-A0R7 
       65.75        60.53        28.27        54.02        37.91        17.59 
TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M 
       36.33        66.15        28.64        14.96        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3QS 
       14.43        34.16        18.90        33.90         1.64        16.87 
TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A3K1 
       16.87        63.91        45.53        48.79        46.78        21.90 
TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CK 
       36.13        80.55        35.74        37.78        34.65        80.25 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A3FW 
        4.77        30.12        40.80        81.37        17.75         0.56 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K7 TCGA-B5-A0K9 
        0.30         0.26        55.30        58.75        63.55        13.45 
TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 
       75.72        50.89        31.36        29.65        19.33        20.94 
TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3EW TCGA-BG-A3PP 
       15.42        52.83        15.45        23.70        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        31.00        24.13        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A168 
       72.72        73.25        63.58        83.64        29.95        36.10 
TCGA-D1-A16G TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A2G6 TCGA-D1-A3DH 
       27.42        18.67        28.08        11.15         8.48        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
       17.29       109.08        36.62        35.38       110.10        79.10 
TCGA-EO-A1Y7 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO 
       49.15        26.96        22.26        23.34        32.71        19.27 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY 
       22.03        11.08        29.10        11.38        14.70        68.38 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       77.33         7.99        28.93        30.67        41.56        78.38 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       17.75        14.04         9.47        38.70         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK  6(2P24.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3IA 
       41.06        88.18        60.53        30.15        16.83        20.81 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
      110.63        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0YV 
       36.39        61.18        80.38        27.09        61.87        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A1GQ 
       14.27         1.81         4.44        47.84        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        17.92        19.89        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 
       36.00         0.43        39.52        10.29       106.88        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX 
       74.10        46.55        73.87        36.82        23.21        68.65 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       31.99        33.07       118.19        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       11.21        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       18.12        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
      129.80        21.99        23.31        86.07        48.03        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        60.23        45.86        27.85        51.12         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        33.21        29.69        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        61.08        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2HC 
       76.83        85.48        73.41        37.58        71.24        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 
        0.23         0.20        43.82         0.20        20.52         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       59.24        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11E 
       72.62        27.29        57.76        64.21        27.85        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 
       41.06        34.13        34.95        18.61        20.19        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        52.01        34.29        52.64        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2L7 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       20.12        34.98        35.90        35.08        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0V4 
       92.88       114.90        85.84        82.39        81.57        59.51 
TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       89.59        86.99        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
        1.78        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95        48.79        58.95        15.88         4.27 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20        71.61       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT 
       25.91        16.31        39.29        24.30         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GP 
       24.36        27.16        23.34        23.90        33.34        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        16.11        32.78        15.81        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D6 TCGA-FI-A2EU 
       32.52        14.14        16.96        39.88        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 
       59.01         9.34        59.28         1.74        13.28        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       18.21        23.24        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                       149.56                        225.50 
  AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE 
                        28.08                         30.74 
[1] "0.1 - 149.6 (28.1)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.6"
D6V2, binary
                               cls
clus                              0   1
  AMP PEAK  6(2P24.3) MUTATED    62  51
  AMP PEAK  6(2P24.3) WILD-TYPE 228 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(2P24.3) MUTATED     62   51
  AMP PEAK  6(2P24.3) WILD-TYPE  228  173
     clus
vv    AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE
  NO                           62                           228
  YES                          51                           173
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  6(2P24.3) MUTATED                                        56
  AMP PEAK  6(2P24.3) WILD-TYPE                                     348
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  6(2P24.3) MUTATED                               8
  AMP PEAK  6(2P24.3) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  6(2P24.3) MUTATED                                  58
  AMP PEAK  6(2P24.3) WILD-TYPE                                55
D6V3, multiclass
                                         clus
vv                                        AMP PEAK  6(2P24.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          56
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                58
                                         clus
vv                                        AMP PEAK  6(2P24.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           348
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(2P24.3) MUTATED    84   5   5  11
  AMP PEAK  6(2P24.3) WILD-TYPE 287  17  11  29
D6V4, multiclass
    clus
vv   AMP PEAK  6(2P24.3) MUTATED AMP PEAK  6(2P24.3) WILD-TYPE
  R0                          84                           287
  R1                           5                            17
  R2                           5                            11
  RX                          11                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(2Q13) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(2Q13) MUTATED    80  38
  AMP PEAK  7(2Q13) WILD-TYPE 367  52
  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                        118                         419 
  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                         38                          52 
$`AMP PEAK  7(2Q13) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 
       20.81        10.19        57.80        23.05        61.18         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-D1-A0ZO TCGA-D1-A3JP 
       80.38        27.09        22.06        51.55        19.79        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 
       33.30         6.21        14.40        23.74        39.52       149.56 
TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A0GV TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG 
       37.02        60.53        54.02        37.91        17.59        31.99 
TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        28.64        14.96        18.41        20.25        14.43 
TCGA-AJ-A3BK TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       33.90        22.26        16.87        45.53        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IW 
       97.71        46.78        21.90        36.13        80.55        37.78 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IO 
        4.77        30.12        71.24        17.75         2.96        64.93 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K7 TCGA-B5-A0K9 
        0.30         0.39        55.30        27.29        63.55        13.45 
TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M2 
       75.72        50.89        29.65        34.13        34.95        20.94 
TCGA-BG-A0RY TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 
       15.42        23.70        22.39        35.90        35.08        31.00 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-D1-A0ZP 
       24.13        16.64         4.80        72.72        63.58        29.95 
TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NX 
       36.10        11.51        14.73        11.15        13.22        18.25 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR 
        8.48        58.95        15.88        18.84        17.29        71.61 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A2CG 
       35.38         9.37       110.10        79.10        10.92        51.42 
TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GH 
       19.40        26.96        22.26        16.34        54.15        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A2OQ TCGA-EY-A3QX 
       23.90        32.71        19.27        22.03        29.10        32.52 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2F8 
       11.38        14.70        68.38        77.33         7.99        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       59.28        41.56        78.38        17.75        14.04         9.47 
TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A8F1 
       18.21        38.70        22.59         4.44 

$`AMP PEAK  7(2Q13) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       18.08       110.63        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2HF TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 
       36.39        27.88        66.41        61.87        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
        1.81         4.44        47.84        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 
       73.32        36.00         0.43        10.29       106.88        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW 
       65.75        46.55        73.87        36.82        28.27        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       31.99        33.07       118.19        66.15        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       25.51        11.21        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        34.16        18.12        18.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.62        20.91       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        51.12         0.56        13.58        33.21        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       25.51        26.37        32.02        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA 
       85.48        73.41        80.25        37.58        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       34.32        46.49        38.24        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 
        0.20         0.56        43.82         0.20        20.52         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11E 
       36.49        72.62        57.76        64.21        27.85        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 
       27.65        41.06        18.61        20.19        19.33        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB 
        9.57        20.02        20.12        11.31        34.98        35.90 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 
       82.39        81.57        73.25        59.51        89.59        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       86.99        66.48        16.83         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
        1.78        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       48.79         4.27         2.20       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30        12.39        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       45.57        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        18.84        17.62        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A5W2 
       20.05        45.76        31.04        27.35        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88        25.22        96.69        59.01         9.34        28.93 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 
        1.74        13.28        26.10        23.24        21.30         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        20.75        18.28         0.07         0.23 

  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                       0.30                        0.07 
  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                     149.56                      225.50 
  AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE 
                     27.025                      30.440 
[1] "0.3 - 149.6 (27.0)" "0.1 - 225.5 (30.4)"
[1] "hr=" "2.9"
D7V2, binary
                             cls
clus                            0   1
  AMP PEAK  7(2Q13) MUTATED    56  56
  AMP PEAK  7(2Q13) WILD-TYPE 234 168
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(2Q13) MUTATED     56   56
  AMP PEAK  7(2Q13) WILD-TYPE  234  168
     clus
vv    AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE
  NO                         56                         234
  YES                        56                         168
[1] 2 2
[1] FALSE
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  7(2Q13) MUTATED                                        45
  AMP PEAK  7(2Q13) WILD-TYPE                                     359
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  7(2Q13) MUTATED                               6
  AMP PEAK  7(2Q13) WILD-TYPE                            16
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  7(2Q13) MUTATED                                  68
  AMP PEAK  7(2Q13) WILD-TYPE                                45
D7V3, multiclass
                                         clus
vv                                        AMP PEAK  7(2Q13) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        45
  MIXED SEROUS AND ENDOMETRIOID                                   6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              68
                                         clus
vv                                        AMP PEAK  7(2Q13) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         359
  MIXED SEROUS AND ENDOMETRIOID                                    16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  7(2Q13) MUTATED    78   5   7  10
  AMP PEAK  7(2Q13) WILD-TYPE 293  17   9  30
D7V4, multiclass
    clus
vv   AMP PEAK  7(2Q13) MUTATED AMP PEAK  7(2Q13) WILD-TYPE
  R0                        78                         293
  R1                         5                          17
  R2                         7                           9
  RX                        10                          30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(3P25.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(3P25.1) MUTATED    62  20
  AMP PEAK  8(3P25.1) WILD-TYPE 385  70
  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                           82                           455 
  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                           20                            70 
$`AMP PEAK  8(3P25.1) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A06D 
       29.39        20.81        10.19        93.99        67.66        12.26 
TCGA-B5-A0JN TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A72D 
       80.38        47.84        33.30        17.88        10.19         5.88 
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A2K2 
       39.52        37.02        65.75        36.82        36.33       118.19 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3QS TCGA-AJ-A8CW 
       18.41        14.43        21.14        34.16        16.87         0.13 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LO TCGA-AP-A1DO 
       63.91        36.89       125.42        36.36        33.40        31.30 
TCGA-AX-A05W TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A3G4 TCGA-AX-A3G6 
       80.55         4.77        30.12        40.80         0.30         0.26 
TCGA-AX-A3GI TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A3FB 
        0.39        57.76        77.23       225.50        11.87        93.50 
TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV 
       34.95        71.24        15.42        52.83        92.88        73.25 
TCGA-BS-A0V8 TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 
       83.64        18.67        14.73        13.22        18.25         2.07 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DI-A2QU TCGA-DI-A2QY 
        8.48        58.95        18.84        17.29        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3B1 
       79.10        10.92        37.71        51.52        34.39        26.96 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A4KR 
       22.26        54.15        17.62        22.03        11.08        11.38 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ 
       59.01         9.34        30.67        59.28        78.38        14.04 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
       38.70        22.59         8.19        14.83 

$`AMP PEAK  8(3P25.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
      110.63        57.80        95.47        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       27.88         1.38        27.09        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       16.93         6.21        22.78        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       19.89        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN 
       32.78       112.54       105.37       123.68        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 
       15.95        31.99        31.99        33.07        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23M 
       24.72        34.95        25.51        14.96        11.21        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI 
       10.26        19.79        35.15        34.36        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       14.76        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       45.53        23.87        12.62        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        33.21        29.69        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC 
       73.41        80.25        37.58        71.24        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
       20.52         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        27.29        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       52.04        32.09        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        52.54        31.36       136.60        96.30 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        29.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 
       18.61        20.19        19.33        20.94        35.21        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        21.17        20.28        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.08        31.00        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       72.72        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        0.72        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
       48.79        15.88         4.27         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        49.15        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.42        19.40        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        16.34        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       33.34        32.71        19.27        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       45.76        31.04        29.10        27.35        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
       25.22        96.69        28.93        41.56         1.74        17.75 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        21.30 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                         0.13                          0.07 
  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                       225.50                        185.79 
  AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE 
                        31.20                         29.65 
[1] "0.1 - 225.5 (31.2)" "0.1 - 185.8 (29.6)"
[1] "hr=" "1.5"
D8V2, binary
                               cls
clus                              0   1
  AMP PEAK  8(3P25.1) MUTATED    43  33
  AMP PEAK  8(3P25.1) WILD-TYPE 247 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(3P25.1) MUTATED     43   33
  AMP PEAK  8(3P25.1) WILD-TYPE  247  191
     clus
vv    AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE
  NO                           43                           247
  YES                          33                           191
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  8(3P25.1) MUTATED                                        36
  AMP PEAK  8(3P25.1) WILD-TYPE                                     368
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  8(3P25.1) MUTATED                               2
  AMP PEAK  8(3P25.1) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  8(3P25.1) MUTATED                                  44
  AMP PEAK  8(3P25.1) WILD-TYPE                                69
D8V3, multiclass
                                         clus
vv                                        AMP PEAK  8(3P25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          36
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                44
                                         clus
vv                                        AMP PEAK  8(3P25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           368
  MIXED SEROUS AND ENDOMETRIOID                                      20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(3P25.1) MUTATED    57   3   4   4
  AMP PEAK  8(3P25.1) WILD-TYPE 314  19  12  36
D8V4, multiclass
    clus
vv   AMP PEAK  8(3P25.1) MUTATED AMP PEAK  8(3P25.1) WILD-TYPE
  R0                          57                           314
  R1                           3                            19
  R2                           4                            12
  RX                           4                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(3P14.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(3P14.1) MUTATED    45  20
  AMP PEAK  9(3P14.1) WILD-TYPE 402  70
  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                           65                           472 
  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                           20                            70 
$`AMP PEAK  9(3P14.1) MUTATED`
TCGA-AP-A05D TCGA-AX-A06D TCGA-BG-A0YV TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GQ 
       57.80        12.26        12.56        47.84        33.30        17.88 
TCGA-EY-A212 TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 
       10.19         5.88        39.52        37.91       118.19        28.64 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW 
       21.14        34.16         1.64        16.87        16.87         0.13 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HK 
       33.40        31.30        80.55        30.12        40.80         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A0K3 
       64.93         0.56         0.30         0.26         0.30        27.29 
TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A3FB TCGA-B5-A5OD 
       57.76        77.23       225.50        11.87        93.50        34.13 
TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 
       71.24        15.42        52.83        92.88        73.25        83.64 
TCGA-D1-A16G TCGA-D1-A179 TCGA-D1-A1O0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DG 
       27.42        14.73         2.07         8.48        58.95         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A22Y 
       18.84        17.29       109.08        12.39       110.10        51.52 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GS TCGA-EY-A1GW TCGA-FI-A2CY 
       27.16        26.96        54.15        22.03        11.08        68.38 
TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-QS-A744 TCGA-QS-A8F1 
       59.01        59.28        78.38        14.83         4.44 

$`AMP PEAK  9(3P14.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81        10.19       110.63        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       67.66        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP TCGA-EY-A1G7 
       14.27         1.81        19.79         4.44        16.93         6.21 
TCGA-EY-A1GK TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX 
       22.78        14.40        18.87        17.92        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 
       13.84        73.32        36.00        23.74         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 
       15.95        31.99        31.99        36.33        33.07        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        14.43        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.12        18.90        33.90        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       97.71        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        32.91        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58         4.77        71.24        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       38.24        17.75        30.74        31.13         0.23         0.20 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82         0.20        20.52         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        52.04        32.09        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       51.45        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.30        43.04        59.74        21.17        20.28        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       81.57        72.72        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DA TCGA-DF-A2KN 
       15.06         1.05         3.95        48.79        15.88         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
       71.61       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       19.40        34.39        50.73        35.15        38.07        46.42 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       32.71        19.27        18.84        17.62        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.14        14.70        16.96        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       25.22        96.69         9.34        28.93        30.67        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        21.30        38.70        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                         0.13                          0.07 
  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                       225.50                        185.79 
  AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE 
                       28.640                        29.935 
[1] "0.1 - 225.5 (28.6)" "0.1 - 185.8 (29.9)"
[1] "hr=" "2.1"
D9V2, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P14.1) MUTATED    32  26
  AMP PEAK  9(3P14.1) WILD-TYPE 258 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P14.1) MUTATED     32   26
  AMP PEAK  9(3P14.1) WILD-TYPE  258  198
     clus
vv    AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE
  NO                           32                           258
  YES                          26                           198
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  9(3P14.1) MUTATED                                        34
  AMP PEAK  9(3P14.1) WILD-TYPE                                     370
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  9(3P14.1) MUTATED                               3
  AMP PEAK  9(3P14.1) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  9(3P14.1) MUTATED                                  28
  AMP PEAK  9(3P14.1) WILD-TYPE                                85
D9V3, multiclass
                                         clus
vv                                        AMP PEAK  9(3P14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          34
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                28
                                         clus
vv                                        AMP PEAK  9(3P14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           370
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(3P14.1) MUTATED    40   5   3   4
  AMP PEAK  9(3P14.1) WILD-TYPE 331  17  13  36
D9V4, multiclass
    clus
vv   AMP PEAK  9(3P14.1) MUTATED AMP PEAK  9(3P14.1) WILD-TYPE
  R0                          40                           331
  R1                           5                            17
  R2                           3                            13
  RX                           4                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(3Q26.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(3Q26.2) MUTATED   130  45
  AMP PEAK 10(3Q26.2) WILD-TYPE 317  45
  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                          175                           362 
  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                           45                            45 
$`AMP PEAK 10(3Q26.2) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A1OK TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D 
       41.06        30.15        29.39        20.81       110.63        57.80 
TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       93.99        67.66        12.26        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0YV TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A212 
       12.56        47.84        16.93        33.30        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-5B-A90C 
       14.40        17.92         5.88        66.77        23.74        39.52 
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       37.02        65.75        36.82        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BI 
       66.15        14.96        20.25        14.43        34.16        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW 
        1.64        22.26        17.06        15.62        16.87        16.87 
TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       20.78         0.13        21.99        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A5FX 
      125.42        97.71        33.40        31.30        46.78        36.13 
TCGA-AW-A1PO TCGA-AX-A05W TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA 
        0.56        80.55        35.74        37.78        34.65        32.02 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HK 
       76.83         4.77        30.12        71.24        40.80         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
       64.93         0.56        43.82        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JX TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A11H 
        0.30         0.39        58.75        27.29        57.76        88.34 
TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FH 
       75.72        77.23       225.50        11.87        31.36        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0MT TCGA-BG-A0RY 
       29.65        34.13        34.95        71.24        21.17        15.42 
TCGA-BG-A0W1 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0U9 
       52.83        22.39        35.08        31.00         4.80        92.88 
TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A15V TCGA-D1-A168 TCGA-D1-A16G 
       73.25        83.64        29.95        39.48        36.10        27.42 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A176 TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU 
       31.07        18.67        30.15        14.73        28.08        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        0.72        18.25         2.07         8.48        58.95        15.88 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.84        17.29        71.61       109.08        25.91        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A1Y5 
        9.37        31.10       110.10        79.10         7.36        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AV 
       49.15        37.71        51.52        51.42        34.39        35.15 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO 
       26.96        22.26        16.34        23.90        32.71        19.27 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A3L3 
       17.62        22.03        15.81        11.08        20.05        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW 
       32.52        11.38        14.70        68.38        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
        9.34        28.93        30.67        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 
       23.24        38.70        22.59         8.19        14.83         4.44 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK 10(3Q26.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A0LS 
       88.18        60.53        16.83        18.08        10.19        95.47 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        51.55        14.27         1.81        19.79         4.44 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 
        6.21        22.78        18.87        19.89        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       36.00         0.43        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A2K5 
       42.35        15.95        31.99        33.07        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK 
       34.95        25.51        11.21        18.41        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK 
       19.79        35.15        34.36        18.12        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       22.49        36.99        20.65        21.21        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 
       14.76        22.32        12.82         2.70        35.11       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07        48.03        63.91        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR 
       25.08        71.67        90.97        55.89        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        33.21        29.69        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        61.08        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       32.91        25.51        26.37        25.91        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       73.41        80.25        37.58        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       38.24        17.75        30.74        31.13         0.23         0.20 
TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.20         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       55.30        59.24        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       36.49        72.62        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
       59.84       185.79       113.36        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        52.04        32.09        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       51.45        14.70        48.43        52.54       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       93.50        71.84        39.35        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       19.33        20.94        35.21        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       20.28        51.06        52.01        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       34.98        35.90        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KN 
       15.06         1.05         3.95        48.79         4.27         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        12.39        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       45.57        16.04        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ 
       46.26        57.60        19.40        50.73        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       46.42        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GP 
       24.36        27.16        23.34        23.34        33.34        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       16.11        32.78        37.05        19.33        12.59        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 
       45.76        31.04        29.10        14.14        16.96        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2F9 TCGA-PG-A6IB TCGA-PG-A916 
       77.33         7.99        25.22        59.28        21.30        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI 
        6.97        22.65        39.95        24.95        23.64        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                       225.50                        185.79 
  AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE 
                        28.93                         30.26 
[1] "0.1 - 225.5 (28.9)" "0.2 - 185.8 (30.3)"
[1] "hr=" "2.3"
D10V2, binary
                               cls
clus                              0   1
  AMP PEAK 10(3Q26.2) MUTATED    81  81
  AMP PEAK 10(3Q26.2) WILD-TYPE 209 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3Q26.2) MUTATED     81   81
  AMP PEAK 10(3Q26.2) WILD-TYPE  209  143
     clus
vv    AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE
  NO                           81                           209
  YES                          81                           143
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 10(3Q26.2) MUTATED                                        76
  AMP PEAK 10(3Q26.2) WILD-TYPE                                     328
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 10(3Q26.2) MUTATED                               8
  AMP PEAK 10(3Q26.2) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 10(3Q26.2) MUTATED                                  91
  AMP PEAK 10(3Q26.2) WILD-TYPE                                22
D10V3, multiclass
                                         clus
vv                                        AMP PEAK 10(3Q26.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          76
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                91
                                         clus
vv                                        AMP PEAK 10(3Q26.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           328
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(3Q26.2) MUTATED   114   8   9  14
  AMP PEAK 10(3Q26.2) WILD-TYPE 257  14   7  26
D10V4, multiclass
    clus
vv   AMP PEAK 10(3Q26.2) MUTATED AMP PEAK 10(3Q26.2) WILD-TYPE
  R0                         114                           257
  R1                           8                            14
  R2                           9                             7
  RX                          14                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(3Q26.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(3Q26.2) MUTATED   122  42
  AMP PEAK 11(3Q26.2) WILD-TYPE 325  48
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          164                           373 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                           42                            48 
$`AMP PEAK 11(3Q26.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       41.06        29.39        20.81       110.63        57.80        93.99 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A2G5 
       80.38        27.09        22.06        66.41        12.56        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 
       16.93        33.30        17.88        10.19        14.40        17.92 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ 
        5.88        66.77        23.74        39.52        37.02        65.75 
TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A3LP 
       36.82        31.99        36.33       118.19        66.15        14.96 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       18.41        20.25        14.43        34.16        18.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A052 
        1.64        22.26        16.87        16.87         0.13        21.99 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO 
       45.53        36.89        48.79       125.42        97.71        33.40 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05W TCGA-AX-A0IW 
       31.30        46.78        36.13         0.56        80.55        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       34.65        32.02        76.83         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       40.80         2.96        64.93         0.56        43.82        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JX TCGA-B5-A0K3 TCGA-B5-A0K4 
        0.30         0.26         0.39        58.75        27.29        57.76 
TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 
       59.84        75.72        77.23       225.50        11.87        31.36 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 
       34.13        34.95        71.24        21.17        15.42        52.83 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV 
       22.39        35.08        31.00         4.80        92.88        73.25 
TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A15V TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I 
       83.64        29.95        39.48        36.10        27.42        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A176 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW 
       31.07        18.67        30.15        28.08        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ 
       18.25         8.48        58.95        15.88        18.84        17.29 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
       71.61       109.08        25.91        35.38         9.37       110.10 
TCGA-E6-A1LZ TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y 
       79.10         7.36        10.92        49.15        37.71        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       51.42        34.39        26.96        22.26        16.34        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV 
       23.90        32.71        19.27        17.62        22.03        15.81 
TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A 
       11.08        20.05        27.35        32.52        11.38        14.70 
TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       68.38        96.69        59.01         9.34        28.93        30.67 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56        78.38        17.75        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 
       26.10        23.24        38.70        22.59         8.19        14.83 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`AMP PEAK 11(3Q26.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3NH 
       88.18        60.53        30.15        16.83        18.08        10.19 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
       95.47        67.66        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A215 TCGA-EY-A549 
       19.79         4.44         6.21        22.78        18.87        19.89 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      149.56        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
      123.68        74.10        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95        31.99        33.07 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23O 
       28.64        24.72        34.95        25.51        11.21        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK 
       21.14        19.79        35.15        34.36        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.70        35.11       129.80        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       63.91        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       55.89        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        51.12        21.90        13.58        33.21        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       26.37        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       37.58        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G7 
       30.74        31.13         0.23         0.20         0.20         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       59.24        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       72.62        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       52.04        32.09        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW 
       71.84        39.35        27.65        29.65        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.19        19.33        20.94        35.21        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       59.74        20.28        51.06        52.01        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98        35.90        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       72.72        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 
        3.68        29.33        32.58         0.66        15.72        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.36        37.51        36.79        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY 
       11.15        24.30         2.33        22.92         1.41        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         2.20       100.83        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G 
       23.38        58.95         2.37        45.57        16.04        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       61.74        61.55        66.90        46.26        57.60        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX 
       50.73        35.15        38.07        27.16        46.42        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       23.34        33.34        18.84        16.11        32.78        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        45.76        31.04        29.10 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        39.88        77.33         7.99        25.22 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       59.28         1.74        18.21        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       22.65        39.95        24.95        23.64        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                       225.50                        185.79 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                        29.16                         30.02 
[1] "0.1 - 225.5 (29.2)" "0.2 - 185.8 (30.0)"
[1] "hr=" "2.1"
D11V2, binary
                               cls
clus                              0   1
  AMP PEAK 11(3Q26.2) MUTATED    76  78
  AMP PEAK 11(3Q26.2) WILD-TYPE 214 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3Q26.2) MUTATED     76   78
  AMP PEAK 11(3Q26.2) WILD-TYPE  214  146
     clus
vv    AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE
  NO                           76                           214
  YES                          78                           146
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 11(3Q26.2) MUTATED                                        68
  AMP PEAK 11(3Q26.2) WILD-TYPE                                     336
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 11(3Q26.2) MUTATED                               8
  AMP PEAK 11(3Q26.2) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 11(3Q26.2) MUTATED                                  88
  AMP PEAK 11(3Q26.2) WILD-TYPE                                25
D11V3, multiclass
                                         clus
vv                                        AMP PEAK 11(3Q26.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          68
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                88
                                         clus
vv                                        AMP PEAK 11(3Q26.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           336
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(3Q26.2) MUTATED   107   8   9  13
  AMP PEAK 11(3Q26.2) WILD-TYPE 264  14   7  27
D11V4, multiclass
    clus
vv   AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE
  R0                         107                           264
  R1                           8                            14
  R2                           9                             7
  RX                          13                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(4P16.3) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(4P16.3) MUTATED    39  13
  AMP PEAK 12(4P16.3) WILD-TYPE 408  77
  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                           52                           485 
  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                           13                            77 
$`AMP PEAK 12(4P16.3) MUTATED`
TCGA-AJ-A2QM TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-EY-A72D TCGA-A5-A0G5 
       29.39         1.38        80.38        22.06         5.88        37.02 
TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BF 
       31.99       118.19        18.41        20.25        14.43        18.12 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AX-A0IU 
       63.91        36.89        48.79       125.42        97.71        35.74 
TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HH 
       34.65        76.83        37.58         4.77        71.24        17.75 
TCGA-AX-A3FW TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-D1-A0ZZ 
        0.56        29.65        34.13        35.08        16.64        22.55 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 
       11.51        31.07        18.67        18.25         2.07        58.95 
TCGA-D1-A3DH TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       18.84       110.10        10.92        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A2OQ 
       34.39        26.96        16.34        23.90        11.08        29.10 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-KP-A3W4 TCGA-PG-A914 
       96.69        59.28        18.21        22.59 

$`AMP PEAK 12(4P16.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       20.81        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       27.09        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       17.92        19.89        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       23.74         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33        33.07        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       25.51        14.96        11.21        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       35.15        34.36        34.16        18.90        33.90         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       45.53        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW 
       57.47        27.39        30.02        60.66        61.08        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       80.25        30.12        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       38.24        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.20        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       39.35        27.65        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       35.90        31.00        31.76        24.99        24.13        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
        4.87        28.67        23.93         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22         0.72        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
        3.95        48.79         8.48        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        27.35        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       25.22        59.01         9.34        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       78.38         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 
       26.10        23.24        21.30        38.70         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                         0.56                          0.07 
  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                       125.42                        225.50 
  AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE 
                       29.245                        30.020 
[1] "0.6 - 125.4 (29.2)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.6"
D12V2, binary
                               cls
clus                              0   1
  AMP PEAK 12(4P16.3) MUTATED    24  26
  AMP PEAK 12(4P16.3) WILD-TYPE 266 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(4P16.3) MUTATED     24   26
  AMP PEAK 12(4P16.3) WILD-TYPE  266  198
     clus
vv    AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE
  NO                           24                           266
  YES                          26                           198
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 12(4P16.3) MUTATED                                        14
  AMP PEAK 12(4P16.3) WILD-TYPE                                     390
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 12(4P16.3) MUTATED                               2
  AMP PEAK 12(4P16.3) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 12(4P16.3) MUTATED                                  36
  AMP PEAK 12(4P16.3) WILD-TYPE                                77
D12V3, multiclass
                                         clus
vv                                        AMP PEAK 12(4P16.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          14
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                36
                                         clus
vv                                        AMP PEAK 12(4P16.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           390
  MIXED SEROUS AND ENDOMETRIOID                                      20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(4P16.3) MUTATED    35   3   4   2
  AMP PEAK 12(4P16.3) WILD-TYPE 336  19  12  38
D12V4, multiclass
    clus
vv   AMP PEAK 12(4P16.3) MUTATED AMP PEAK 12(4P16.3) WILD-TYPE
  R0                          35                           336
  R1                           3                            19
  R2                           4                            12
  RX                           2                            38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(5P15.33) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(5P15.33) MUTATED    60  28
  AMP PEAK 13(5P15.33) WILD-TYPE 387  62
  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                            88                            449 
  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                            28                             62 
$`AMP PEAK 13(5P15.33) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 
       20.81        10.19        61.18         1.38        80.38        22.06 
TCGA-BG-A0VT TCGA-E6-A8L9 TCGA-EY-A547 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-5B-A90C 
       51.55        33.30        17.92         5.88        23.74        39.52 
TCGA-A5-A0G5 TCGA-A5-A0GB TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N 
       37.02        32.78        65.75        36.33        14.96        14.43 
TCGA-AJ-A2QK TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 
       21.14        22.26        16.87        16.87        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AW-A1PO 
      125.42        36.36        97.71        31.30        46.78         0.56 
TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ 
       61.08        37.78         4.77        71.24         2.96         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A5OD 
       20.52         0.30         0.39        11.87        39.35        34.13 
TCGA-B5-A5OE TCGA-BG-A0M3 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
       34.95        35.21        15.45        22.39        35.08        31.00 
TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A16N TCGA-D1-A179 
       24.13         4.80        83.64        39.48        31.07        14.73 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DI-A1NN 
       13.22         0.72        18.25        18.84        17.29        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
        9.37        12.39        31.10       110.10        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GJ 
       37.71        51.42        26.96        22.26        54.15        23.90 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 
       17.62        22.03        20.05        32.52        11.38        77.33 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI 
       59.01         9.34        28.93        30.67         1.74        17.75 
TCGA-K6-A3WQ TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       14.04        22.59         8.19         4.44 

$`AMP PEAK 13(5P15.33) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M8 
       12.26        36.39        23.05        27.88        27.09        66.41 
TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       47.84        16.93         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       14.40        18.87        19.89        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       36.00         0.43        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN 
       17.85       112.54       105.37       123.68        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        31.99        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ 
       66.15        28.64        24.72        34.95        25.51        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       18.41        20.25        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16        18.12        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
       20.91       117.99       110.37        66.25        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR 
       25.08        71.67        90.97        55.89        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        30.12        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.23         0.20         0.56        43.82         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       51.45        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        93.50        71.84        27.65        29.65        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 
       18.61        20.19        19.33        20.94        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        85.55        78.21        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        2.33        22.92         1.41        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
       15.88         4.27         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       36.62        24.30        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW 
       50.73        35.15        38.07        27.16        46.42        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        33.34        32.71        19.27        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       12.59        22.82        45.76        31.04        29.10        27.35 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W0 
       25.22        96.69        59.28        41.56        78.38        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        9.47        26.10        18.21        23.24        21.30        38.70 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        20.75        18.28         0.07         0.23 

  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                          0.20                           0.07 
  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                        125.42                         225.50 
  AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE 
                        23.165                         30.150 
[1] "0.2 - 125.4 (23.2)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.8"
D13V2, binary
                                cls
clus                               0   1
  AMP PEAK 13(5P15.33) MUTATED    41  39
  AMP PEAK 13(5P15.33) WILD-TYPE 249 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(5P15.33) MUTATED     41   39
  AMP PEAK 13(5P15.33) WILD-TYPE  249  185
     clus
vv    AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE
  NO                            41                            249
  YES                           39                            185
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 13(5P15.33) MUTATED                                        30
  AMP PEAK 13(5P15.33) WILD-TYPE                                     374
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 13(5P15.33) MUTATED                               3
  AMP PEAK 13(5P15.33) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 13(5P15.33) MUTATED                                  56
  AMP PEAK 13(5P15.33) WILD-TYPE                                57
D13V3, multiclass
                                         clus
vv                                        AMP PEAK 13(5P15.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           30
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 56
                                         clus
vv                                        AMP PEAK 13(5P15.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            374
  MIXED SEROUS AND ENDOMETRIOID                                       19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(5P15.33) MUTATED    58   3   6   8
  AMP PEAK 13(5P15.33) WILD-TYPE 313  19  10  32
D13V4, multiclass
    clus
vv   AMP PEAK 13(5P15.33) MUTATED AMP PEAK 13(5P15.33) WILD-TYPE
  R0                           58                            313
  R1                            3                             19
  R2                            6                             10
  RX                            8                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(5Q35.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(5Q35.3) MUTATED    38  18
  AMP PEAK 14(5Q35.3) WILD-TYPE 409  72
  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                           56                           481 
  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                           18                            72 
$`AMP PEAK 14(5Q35.3) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A2H8 
       29.39        10.19       110.63        57.80        67.66        61.18 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-A5-A7WK TCGA-AJ-A23N 
        1.38        80.38        22.06        51.55        18.41        14.43 
TCGA-AJ-A3BF TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A1DO TCGA-AP-A3K1 TCGA-AX-A0IS 
       18.12        16.87        20.78        31.30        21.90        61.08 
TCGA-AX-A1C8 TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3GI 
       25.51         4.77        71.24         0.56        20.52         0.39 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0TI 
       11.87        31.36        15.45        22.39         4.80        61.87 
TCGA-D1-A16G TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3JQ 
       27.42         0.72        18.25         2.07         4.27        17.29 
TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EY-A1GR 
       71.61        25.91        35.38        79.10        10.92        17.62 
TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2EU 
       22.03        12.59        29.10        27.35        14.70        96.69 
TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-PG-A7D5 
       59.01        59.28         1.74        17.75        14.04        38.70 
TCGA-PG-A914 TCGA-QS-A8F1 
       22.59         4.44 

$`AMP PEAK 14(5Q35.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR 
       20.81        93.99        95.47        12.26        36.39        23.05 
TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 
       27.88        27.09        66.41        61.87        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       15.95        31.99        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        20.25        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        34.16        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.62        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ 
       25.08        71.67        90.97        55.89        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IW 
       57.47        27.39        30.02        60.66        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        30.12        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20        43.82         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       52.54       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       27.65        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.08        31.00        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
       22.92         1.41        13.22        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       18.84         2.20       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10       110.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       45.57        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       18.84        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       19.33        22.82        20.05        45.76        31.04        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       11.38        14.14        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
        7.99        25.22         9.34        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       78.38        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                         0.39                          0.07 
  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                       110.63                        225.50 
  AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE 
                       21.965                        30.740 
[1] "0.4 - 110.6 (22.0)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.8"
D14V2, binary
                               cls
clus                              0   1
  AMP PEAK 14(5Q35.3) MUTATED    28  24
  AMP PEAK 14(5Q35.3) WILD-TYPE 262 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(5Q35.3) MUTATED     28   24
  AMP PEAK 14(5Q35.3) WILD-TYPE  262  200
     clus
vv    AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE
  NO                           28                           262
  YES                          24                           200
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 14(5Q35.3) MUTATED                                        22
  AMP PEAK 14(5Q35.3) WILD-TYPE                                     382
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 14(5Q35.3) MUTATED                               3
  AMP PEAK 14(5Q35.3) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 14(5Q35.3) MUTATED                                  32
  AMP PEAK 14(5Q35.3) WILD-TYPE                                81
D14V3, multiclass
                                         clus
vv                                        AMP PEAK 14(5Q35.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          22
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                32
                                         clus
vv                                        AMP PEAK 14(5Q35.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           382
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(5Q35.3) MUTATED    35   3   3   5
  AMP PEAK 14(5Q35.3) WILD-TYPE 336  19  13  35
D14V4, multiclass
    clus
vv   AMP PEAK 14(5Q35.3) MUTATED AMP PEAK 14(5Q35.3) WILD-TYPE
  R0                          35                           336
  R1                           3                            19
  R2                           3                            13
  RX                           5                            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(6P24.2) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(6P24.2) MUTATED    87  30
  AMP PEAK 15(6P24.2) WILD-TYPE 360  60
  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                          117                           420 
  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                           30                            60 
$`AMP PEAK 15(6P24.2) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CR 
       20.81        10.19       110.63        57.80        67.66        23.05 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GQ 
        1.38        80.38        66.41        47.84        33.30        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-FI-A2CX TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GR 
       10.19        14.40        66.77        39.52        37.02        36.82 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       31.99        36.33       118.19        14.96        20.25        14.43 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW 
       34.16        18.12        18.90         1.64        16.87        16.87 
TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
        0.13        63.91        45.53        48.79       125.42        97.71 
TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A1C7 
       33.40        46.78        36.13        30.02        37.78        34.65 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       32.02        25.91        76.83        30.12        40.80        81.37 
TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JS 
       64.93        43.82        20.52         0.26         0.39        86.37 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A11S 
       27.29        27.85        59.84        75.72        77.23        73.28 
TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       50.89        31.36        93.50        29.65        34.13        34.95 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       15.45        35.90        35.08        24.13        16.64        92.88 
TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NW 
       83.64        36.10        31.07        18.67        14.73         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2KY 
        2.07         4.27        18.84        17.29       109.08        10.92 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A22Y 
       25.91        35.38        31.10       110.10        37.71        51.52 
TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO 
       51.42        26.96        22.26        16.34        54.15        19.27 
TCGA-EY-A1GR TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2D0 
       17.62        20.05        29.10        27.35        32.52        39.88 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       77.33        96.69        59.01         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       59.28        78.38        14.04        26.10        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        8.19         4.44         0.07 

$`AMP PEAK 15(6P24.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
       18.08        93.99        95.47        12.26        36.39        61.18 
TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       27.88        27.09        22.06        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP TCGA-EY-A1G7 
       14.27         1.81        19.79         4.44        16.93         6.21 
TCGA-EY-A1GK TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 
       22.78        18.87        17.92        19.89         5.88        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00        23.74         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      149.56        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       34.36        33.90        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       14.76        22.32        12.82        20.78         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
      129.80        21.99        23.31        86.07        48.03        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.62        20.91       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        51.12        21.90         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       79.46        49.87        57.47        27.39        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.51        26.37        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       37.58         4.77        71.24        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74         2.96        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56         0.20         0.30         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       64.21        63.55        13.45       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      225.50       102.31        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
       52.54       136.60        96.30        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.90        31.00        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       11.51        29.92        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
        8.48        58.95        15.88         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       89.33        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        12.39        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       61.74        61.55        66.90        46.26        57.60        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        32.71        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       22.03        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR 
       19.33        12.59        22.82        45.76        31.04        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        14.70        16.96        68.38         7.99        25.22 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 
       41.56         1.74        17.75        13.28         9.47        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64        14.83        20.75        18.28         0.23 

  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                       125.42                        225.50 
  AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE 
                       32.020                        28.455 
[1] "0.1 - 125.4 (32.0)" "0.2 - 225.5 (28.5)"
[1] "hr=" "1.7"
D15V2, binary
                               cls
clus                              0   1
  AMP PEAK 15(6P24.2) MUTATED    64  47
  AMP PEAK 15(6P24.2) WILD-TYPE 226 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(6P24.2) MUTATED     64   47
  AMP PEAK 15(6P24.2) WILD-TYPE  226  177
     clus
vv    AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE
  NO                           64                           226
  YES                          47                           177
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 15(6P24.2) MUTATED                                        47
  AMP PEAK 15(6P24.2) WILD-TYPE                                     357
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 15(6P24.2) MUTATED                               5
  AMP PEAK 15(6P24.2) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 15(6P24.2) MUTATED                                  65
  AMP PEAK 15(6P24.2) WILD-TYPE                                48
D15V3, multiclass
                                         clus
vv                                        AMP PEAK 15(6P24.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          47
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                65
                                         clus
vv                                        AMP PEAK 15(6P24.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           357
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(6P24.2) MUTATED    74   5   5  10
  AMP PEAK 15(6P24.2) WILD-TYPE 297  17  11  30
D15V4, multiclass
    clus
vv   AMP PEAK 15(6P24.2) MUTATED AMP PEAK 15(6P24.2) WILD-TYPE
  R0                          74                           297
  R1                           5                            17
  R2                           5                            11
  RX                          10                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(6Q25.1) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(6Q25.1) MUTATED    67  21
  AMP PEAK 16(6Q25.1) WILD-TYPE 380  69
  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                           88                           449 
  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                           21                            69 
$`AMP PEAK 16(6Q25.1) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A2G5 
       20.81        10.19        80.38        27.09        66.41        47.84 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-5B-A90C 
       17.88        10.19        14.40        66.77        23.74        39.52 
TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EM 
       14.96        18.41        20.25        35.15        18.90        22.26 
TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX 
        0.13        48.79        97.71        33.40        46.78        36.13 
TCGA-AX-A06J TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A3FW 
       30.02        25.91        30.12        40.80        81.37         0.56 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11E 
       43.82        20.52         0.39        27.29        27.85        59.84 
TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-B5-A5OD 
       75.72        77.23        31.36        93.50        29.65        34.13 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       15.45        35.90        35.08        31.00        24.13        16.64 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A168 TCGA-D1-A16I 
       61.87        92.88        83.64         8.55        36.10        11.51 
TCGA-D1-A16S TCGA-D1-A17K TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.67        28.08        71.61       109.08        25.91        35.38 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU 
       10.92        49.15        57.60        51.52        51.42        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS 
       16.34        54.15        23.90        19.27        17.62        22.03 
TCGA-EY-A1GV TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A 
       15.81        20.05        27.35        32.52        11.38        14.70 
TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       39.88        59.01         9.34        30.67        59.28        78.38 
TCGA-PG-A5BC TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.24         8.19         4.44         0.07 

$`AMP PEAK 16(6Q25.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        16.93        33.30         6.21        22.78 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        17.92        19.89         5.88        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       36.00         0.43        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       31.99        36.33        33.07       118.19        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O 
       24.72        34.95        25.51        11.21        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK 
       21.14        19.79        34.36        34.16        18.12        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       45.53        36.89        23.87        12.62        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD 
       80.25        37.58         4.77        71.24        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.23         0.20         0.20         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       36.49        72.62        57.76        64.21        63.55        13.45 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        52.04        32.09        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
      136.60        96.30        71.84        39.35        27.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98        35.90        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       77.95        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
       32.71        18.84        16.11        32.78        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        45.76        31.04        29.10 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       96.69        28.93        41.56         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28         9.47        26.10        18.21        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.23 

  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                       109.08                        225.50 
  AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE 
                       28.865                        29.950 
[1] "0.1 - 109.1 (28.9)" "0.2 - 225.5 (29.9)"
[1] "hr=" "1.7"
D16V2, binary
                               cls
clus                              0   1
  AMP PEAK 16(6Q25.1) MUTATED    48  35
  AMP PEAK 16(6Q25.1) WILD-TYPE 242 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(6Q25.1) MUTATED     48   35
  AMP PEAK 16(6Q25.1) WILD-TYPE  242  189
     clus
vv    AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE
  NO                           48                           242
  YES                          35                           189
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 16(6Q25.1) MUTATED                                        47
  AMP PEAK 16(6Q25.1) WILD-TYPE                                     357
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 16(6Q25.1) MUTATED                               3
  AMP PEAK 16(6Q25.1) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 16(6Q25.1) MUTATED                                  38
  AMP PEAK 16(6Q25.1) WILD-TYPE                                75
D16V3, multiclass
                                         clus
vv                                        AMP PEAK 16(6Q25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          47
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                38
                                         clus
vv                                        AMP PEAK 16(6Q25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           357
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(6Q25.1) MUTATED    53   1   4  11
  AMP PEAK 16(6Q25.1) WILD-TYPE 318  21  12  29
D16V4, multiclass
    clus
vv   AMP PEAK 16(6Q25.1) MUTATED AMP PEAK 16(6Q25.1) WILD-TYPE
  R0                          53                           318
  R1                           1                            21
  R2                           4                            12
  RX                          11                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(7Q31.2) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(7Q31.2) MUTATED    65  27
  AMP PEAK 17(7Q31.2) WILD-TYPE 382  63
  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                           92                           445 
  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                           27                            63 
$`AMP PEAK 17(7Q31.2) MUTATED`
TCGA-2E-A9G8 TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A3G3 
       41.06        16.83        20.81       110.63        93.99         1.38 
TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-D1-A3JP TCGA-E6-A8L9 
       27.09        66.41        61.87        51.55        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A549 TCGA-EY-A72D TCGA-KP-A3VZ 
        6.21        10.19        14.40        19.89         5.88        23.74 
TCGA-A5-A0GV TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A2QN TCGA-AJ-A3BF 
       54.02        36.33        28.64        14.96        35.15        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       18.90         1.64        15.62        16.87        16.87        20.78 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 
       48.79       125.42        36.36        97.71        33.40        21.90 
TCGA-AX-A05W TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A2H4 TCGA-AX-A2HJ TCGA-AX-A3FZ 
       80.55        25.51        26.37        30.12        30.74         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 
       20.52         0.26         0.39        56.91        55.30        48.59 
TCGA-B5-A0K4 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-BG-A0M3 TCGA-BG-A0RY 
       57.76       102.31        50.89        51.45        35.21        15.42 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       15.45        23.70        35.90        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-D1-A0ZN TCGA-D1-A16I TCGA-D1-A17C TCGA-D1-A17R TCGA-D1-A1NW 
       72.72        16.83        11.51         0.99        11.15         0.72 
TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DI-A1NO TCGA-DI-A2QU 
       16.87         8.48        17.29        71.61         9.37        31.10 
TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GO 
       16.04        37.71        51.52        23.34        33.34        19.27 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       11.08        37.05        11.38        77.33         9.34        28.93 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A915 
       78.38        17.75        14.04        13.28         9.47         8.19 
TCGA-QS-A5YQ TCGA-QS-A8F1 
       24.95         4.44 

$`AMP PEAK 17(7Q31.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3NH 
       88.18        60.53        30.15        29.39        18.08        10.19 
TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR 
       57.80        95.47        67.66        12.26        36.39        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A220 
       61.18        27.88        80.38        22.06        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1GK TCGA-EY-A1GQ 
        1.81        19.79         4.44        47.84        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A547 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       18.87        17.92        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07       118.19        66.15        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       19.79        34.36        34.16        33.90        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ 
       22.26        17.06        36.99        20.65        21.21        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       15.95        14.76        22.32        12.82         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      117.99       110.37        66.25        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        33.21        29.69        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1CA 
       40.11        77.39        13.28        32.91        34.65        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58         4.77        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.23         0.20         0.56        43.82         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
        1.18        18.35        14.47        86.37        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       58.75        69.27        71.44        36.49        72.62        27.29 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.94        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
        9.57        20.02        20.12        11.31        22.39        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       92.88       114.90        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F 
       18.02        14.73         1.58         7.00        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KS 
       58.95        15.88         4.27        18.84         2.20       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        24.30        35.38        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1QX 
       23.38        79.10        58.95         2.37        45.57         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.42        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        38.07        27.16        46.42        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP 
       24.36        27.16        23.34        23.90        32.71        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 
       17.62        22.03        16.11        32.78        15.81        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        32.52        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 
       39.88         7.99        25.22        96.69        59.01        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       59.28        41.56         1.74        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        38.70        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       39.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                       125.42                        225.50 
  AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE 
                        22.62                         31.00 
[1] "0.2 - 125.4 (22.6)" "0.1 - 225.5 (31.0)"
[1] "hr=" "2.5"
D17V2, binary
                               cls
clus                              0   1
  AMP PEAK 17(7Q31.2) MUTATED    49  36
  AMP PEAK 17(7Q31.2) WILD-TYPE 241 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(7Q31.2) MUTATED     49   36
  AMP PEAK 17(7Q31.2) WILD-TYPE  241  188
     clus
vv    AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE
  NO                           49                           241
  YES                          36                           188
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 17(7Q31.2) MUTATED                                        53
  AMP PEAK 17(7Q31.2) WILD-TYPE                                     351
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 17(7Q31.2) MUTATED                               5
  AMP PEAK 17(7Q31.2) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 17(7Q31.2) MUTATED                                  35
  AMP PEAK 17(7Q31.2) WILD-TYPE                                78
D17V3, multiclass
                                         clus
vv                                        AMP PEAK 17(7Q31.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          53
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                35
                                         clus
vv                                        AMP PEAK 17(7Q31.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           351
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(7Q31.2) MUTATED    62   3   4   8
  AMP PEAK 17(7Q31.2) WILD-TYPE 309  19  12  32
D17V4, multiclass
    clus
vv   AMP PEAK 17(7Q31.2) MUTATED AMP PEAK 17(7Q31.2) WILD-TYPE
  R0                          62                           309
  R1                           3                            19
  R2                           4                            12
  RX                           8                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(8P11.22) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(8P11.22) MUTATED    96  30
  AMP PEAK 18(8P11.22) WILD-TYPE 351  60
  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                           126                            411 
  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                            30                             60 
$`AMP PEAK 18(8P11.22) MUTATED`
TCGA-AJ-A3NH TCGA-B5-A0KB TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       10.19        27.09         1.81         4.44        47.84        33.30 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A549 TCGA-A5-A0G5 TCGA-A5-A0GE 
       17.88        14.40        17.92        19.89        37.02       105.37 
TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A3LO 
       23.21        17.59        31.99        33.07        28.64        25.51 
TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI 
       14.96        21.14        19.79        35.15        34.16        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OL 
       33.90         1.64        17.06        20.65        15.62        14.76 
TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LO TCGA-AP-A1DO 
        0.13        63.91        48.79       117.99        33.40        31.30 
TCGA-AP-A1E0 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CI TCGA-AX-A2H2 
       60.23        36.13        37.78        32.02        85.48         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ 
       71.24        40.80        81.37        34.32         0.20         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11Q 
       20.52         0.26        55.30        57.76        59.84        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A3F9 
       77.23        73.28        19.56       102.31        14.70       136.60 
TCGA-B5-A3FD TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA 
       39.35        19.33        20.94        71.24        74.63        10.72 
TCGA-BG-A0MQ TCGA-BG-A0YU TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 
       59.74        14.83        15.45        23.70        22.39        35.90 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0T9 
       35.90        35.08        31.00        24.13        16.64        46.95 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-BS-A0VI 
        4.80        77.95        92.88        73.25        83.64        86.99 
TCGA-D1-A0ZU TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16R 
       28.67         0.66        36.10        37.32        31.07         0.69 
TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G6 
       28.08        11.15        13.22         2.07        48.79         8.48 
TCGA-DF-A2KR TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 
       71.61        24.30        31.10        79.10        58.95        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3B0 
       49.15        66.90        57.60        51.52        19.40        46.42 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR 
       51.09        14.99        54.15        32.71        19.27        17.62 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.81        37.05        19.33        22.82        20.05        29.10 
TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-QS-A744 TCGA-QS-A8F1 
        7.99        59.28        14.04        13.28        14.83         4.44 

$`AMP PEAK 18(8P11.22) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        80.38        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK 
       12.56        14.27        19.79        16.93         6.21        22.78 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       10.19        18.87         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG 
      149.56        83.51        17.85        32.78       112.54       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        68.65        37.91        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A2K2 
       29.06        42.35        15.95        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       66.15        24.72        34.95        11.21        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3EL 
       14.43        10.26        34.36        18.12        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3QS 
       22.26        36.99        21.21        15.35        15.95        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        48.03        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LE 
       36.89        23.87        12.62        20.91       125.42       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        35.54        46.78        49.15         6.71 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        21.90         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        32.91        34.65        25.51        26.37        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       34.09        76.83        73.41        80.25        37.58        30.12 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 
       64.93         0.23         0.56        43.82         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W 
       73.64        61.68        85.78        52.04        16.73        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50        50.89        51.45 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        11.87        52.54        31.36        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       71.84        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG 
       18.61        20.19        35.21        63.68        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       23.47        43.30        43.04        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       20.12        11.31        34.98        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI 
       10.03         9.86        24.33        85.55        78.21        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        72.72        59.51        89.59        63.58 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 
       29.88         1.91         3.68        29.33        32.58        15.72 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       10.22         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        1.05         3.95        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NN 
       27.16        25.91        16.31        39.29        36.62        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 
        9.37        12.39       110.10        23.38         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        37.71        61.74        61.55 
TCGA-EO-A22U TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        51.42        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1GD 
       27.16        26.96        22.26        16.34        38.47        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 
       18.84        22.03        16.11        32.78        11.08        12.59 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        27.35        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 
       14.70        16.96        68.38        39.88        77.33        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       96.69        59.01         9.34        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       78.38         1.74        17.75         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       23.24        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI 
        6.97        22.65        39.95        24.95        23.64        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                          0.13                           0.07 
  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                         136.6                          225.5 
  AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE 
                         30.05                          29.92 
[1] "0.1 - 136.6 (30.1)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.7"
D18V2, binary
                                cls
clus                               0   1
  AMP PEAK 18(8P11.22) MUTATED    70  49
  AMP PEAK 18(8P11.22) WILD-TYPE 220 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(8P11.22) MUTATED     70   49
  AMP PEAK 18(8P11.22) WILD-TYPE  220  175
     clus
vv    AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE
  NO                            70                            220
  YES                           49                            175
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 18(8P11.22) MUTATED                                        94
  AMP PEAK 18(8P11.22) WILD-TYPE                                     310
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 18(8P11.22) MUTATED                               6
  AMP PEAK 18(8P11.22) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 18(8P11.22) MUTATED                                  26
  AMP PEAK 18(8P11.22) WILD-TYPE                                87
D18V3, multiclass
                                         clus
vv                                        AMP PEAK 18(8P11.22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           94
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 26
                                         clus
vv                                        AMP PEAK 18(8P11.22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            310
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(8P11.22) MUTATED    86   4   5  11
  AMP PEAK 18(8P11.22) WILD-TYPE 285  18  11  29
D18V4, multiclass
    clus
vv   AMP PEAK 18(8P11.22) MUTATED AMP PEAK 18(8P11.22) WILD-TYPE
  R0                           86                            285
  R1                            4                             18
  R2                            5                             11
  RX                           11                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(8P11.21) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(8P11.21) MUTATED   120  42
  AMP PEAK 19(8P11.21) WILD-TYPE 327  48
  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                           162                            375 
  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                            42                             48 
$`AMP PEAK 19(8P11.21) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       20.81        10.19        93.99         1.38        80.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GQ 
       66.41         1.81         4.44        47.84        33.30        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A549 TCGA-EY-A72D TCGA-A5-A0G5 TCGA-A5-A0GE 
       10.19        14.40        19.89         5.88        37.02       105.37 
TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A3LO 
       23.21        17.59        31.99        33.07        28.64        25.51 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD 
       14.96        14.43        21.14        19.79        35.15        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OL 
       18.90        33.90         1.64        20.65        15.62        14.76 
TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       16.87         0.13        21.99        45.53        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX 
      117.99        33.40        31.30        60.23        21.90        36.13 
TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A2H2 TCGA-AX-A2H4 
       37.78        32.02        25.91        85.48         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FZ 
       40.80        81.37        34.32        64.93         0.20         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A0K8 
       20.52         0.26         0.39        55.30        57.76        27.85 
TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MS 
       59.84        32.09        77.23        73.28        19.56       102.31 
TCGA-B5-A1MW TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M0 
       14.70        11.87       136.60        39.35        34.95        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MQ TCGA-BG-A0YU 
       20.94        71.24        74.63        10.72        59.74        14.83 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        22.39        35.90        35.90        35.08 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 
       24.13        16.64        46.95         4.80        77.95        92.88 
TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZU TCGA-D1-A15V TCGA-D1-A165 
       73.25        83.64        86.99        28.67        39.48         0.66 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S 
       36.10        37.32        11.51        31.07         0.69        18.67 
TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DH 
       11.15        13.22         2.07        48.79         8.48        18.84 
TCGA-DF-A2KR TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       71.61        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
      110.10        79.10        58.95        10.92        49.15        37.71 
TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B0 TCGA-EO-A3B1 
       66.90        51.52        51.42        19.40        46.42        26.96 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR 
       51.09        14.99        54.15        32.71        19.27        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON 
       22.03        15.81        37.05        19.33        22.82        20.05 
TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
       29.10        77.33         7.99        96.69         9.34        28.93 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       59.28        41.56        17.75        14.04        13.28         9.47 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       38.70        22.59         8.19        14.83         4.44         0.07 

$`AMP PEAK 19(8P11.21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       18.08       110.63        57.80        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0MS 
       36.39        23.05        61.18        27.88        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1G7 
       51.55        12.56        14.27        19.79        16.93         6.21 
TCGA-EY-A1GK TCGA-EY-A215 TCGA-EY-A547 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       22.78        18.87        17.92        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG 
      149.56        83.51        17.85        32.78       112.54       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        68.65        37.91        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A2K2 
       29.06        42.35        15.95        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       66.15        24.72        34.95        11.21        18.41        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       10.26        34.36        18.12        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW 
       17.06        36.99        21.21        15.35        15.95        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 
       22.32        12.82        20.78         2.70        35.11       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       12.62        20.91       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       46.78        49.15         6.71        45.86        27.85        51.12 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       26.37        34.09        76.83        73.41        80.25        37.58 
TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       71.24        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 
       31.13         0.23         0.56        43.82         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18        18.35        14.47        56.91        86.37        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F 
       72.62        27.29        64.21        63.55        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       85.78        52.04        16.73        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       225.50        50.89        51.45        48.43        52.54 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       31.36        96.30        93.50        71.84        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 
       41.06        34.13        18.61        20.19        35.21        63.68 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MT 
       41.52        48.56        23.47        43.30        43.04        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.83        56.58        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A139 
        9.57        20.02        20.12        11.31        34.98        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA 
       31.76        24.99        13.18        10.03         9.86        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       59.51        89.59        63.58        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        8.55         0.56         4.87        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       32.58        15.72        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
       15.06         1.05         3.95        58.95        15.88         4.27 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-E6-A1LX 
       27.16        25.91        16.31        39.29        36.62        23.38 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R 
        2.37        45.57        16.04         7.36        16.80        61.74 
TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       61.55        46.26        57.60        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1GD 
       38.07        27.16        22.26        16.34        38.47        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO 
       18.84        16.11        32.78        11.08        12.59        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F8 
       16.96        68.38        39.88        25.22        59.01        30.67 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       78.38         1.74        26.10        18.21        23.24        21.30 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                          0.07                           0.23 
  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                         136.6                          225.5 
  AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE 
                         27.47                          30.15 
[1] "0.1 - 136.6 (27.5)" "0.2 - 225.5 (30.1)"
[1] "hr=" "2.2"
D19V2, binary
                                cls
clus                               0   1
  AMP PEAK 19(8P11.21) MUTATED    90  60
  AMP PEAK 19(8P11.21) WILD-TYPE 200 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(8P11.21) MUTATED     90   60
  AMP PEAK 19(8P11.21) WILD-TYPE  200  164
     clus
vv    AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE
  NO                            90                            200
  YES                           60                            164
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 19(8P11.21) MUTATED                                        95
  AMP PEAK 19(8P11.21) WILD-TYPE                                     309
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 19(8P11.21) MUTATED                               7
  AMP PEAK 19(8P11.21) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 19(8P11.21) MUTATED                                  60
  AMP PEAK 19(8P11.21) WILD-TYPE                                53
D19V3, multiclass
                                         clus
vv                                        AMP PEAK 19(8P11.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           95
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 60
                                         clus
vv                                        AMP PEAK 19(8P11.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            309
  MIXED SEROUS AND ENDOMETRIOID                                       15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(8P11.21) MUTATED   106   4  11  15
  AMP PEAK 19(8P11.21) WILD-TYPE 265  18   5  25
D19V4, multiclass
    clus
vv   AMP PEAK 19(8P11.21) MUTATED AMP PEAK 19(8P11.21) WILD-TYPE
  R0                          106                            265
  R1                            4                             18
  R2                           11                              5
  RX                           15                             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(8Q24.21) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(8Q24.21) MUTATED   156  51
  AMP PEAK 20(8Q24.21) WILD-TYPE 291  39
  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                           207                            330 
  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                            51                             39 
$`AMP PEAK 20(8Q24.21) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0JN 
       41.06        20.81        10.19        23.05         1.38        80.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 
       27.09        22.06        66.41         1.81         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       33.30        17.88        14.40        17.92        19.89         5.88 
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0GW 
       39.52        37.02       105.37        65.75        36.82        23.21 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 
       17.59        31.99        36.33        33.07       118.19        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QL 
       25.51        14.96        18.41        20.25        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       35.15        34.16        18.12        18.90        33.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OL 
       22.26        17.06        20.65        21.21        15.62        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A05H 
       16.87        16.87        20.78         0.13        63.91        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LO 
       48.79       125.42       117.99        36.36        97.71        33.40 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW 
       31.30        46.78        60.23        21.90         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI 
       34.65        25.51        32.02        25.91        76.83        85.48 
TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       34.32         2.96        64.93         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K4 
        0.20        20.52         0.30         0.39        55.30        57.76 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       59.84        88.34        75.72        32.09        77.23        73.28 
TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1N2 
       19.56       225.50       102.31        50.89        14.70        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 
      136.60        93.50        39.35        34.13        34.95        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MT TCGA-BG-A0YU 
       20.94        71.24        74.63        10.72        21.17        14.83 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC 
       15.45        23.70        22.39        35.90        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TE 
       31.00        24.13        16.64         9.86        46.95         4.80 
TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU 
       77.95        92.88        73.25        86.99        29.95        28.67 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16G 
       22.55        39.48         0.66        36.10        37.32        27.42 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17R 
       11.51        31.07         0.69        18.67        14.73        11.15 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       13.22         0.72         2.07        48.79         8.48        58.95 
TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       18.84        71.61       109.08        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       12.39       110.10        79.10        58.95        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       37.71        66.90        51.52        51.42        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        22.26        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS 
       54.15        23.90        32.71        19.27        17.62        22.03 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.81        37.05        19.33        22.82        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX 
       27.35        32.52        11.38         7.99        96.69         9.34 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        59.28        41.56         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 
       13.28         9.47        26.10        18.21        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A744 TCGA-SL-A6J9 
        8.19        14.83         0.07 

$`AMP PEAK 20(8Q24.21) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
      110.63        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       36.39        61.18        27.88        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A212 
       14.27        19.79        16.93         6.21        22.78        10.19 
TCGA-EY-A215 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       18.87        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP 
       32.78       112.54       123.68        74.10        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       73.87        28.27        54.02        68.65        37.91        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K3 
       24.62        29.06        42.35        15.95        31.99        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QO 
       24.72        34.95        11.21        14.43        10.26        34.36 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV 
       14.66        22.49        36.99        15.35        15.95        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       12.82         2.70        35.11       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07        48.03        36.89        23.87        12.62        20.91 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
      110.37        66.25        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 
       55.89        35.54        49.15         6.71        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       51.12        36.13        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        77.39        13.28        32.91        26.37 
TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       34.09        73.41        37.58        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 
       30.74        31.13         0.23         0.30         0.26         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       18.35        14.47        56.91        86.37        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       27.29        64.21        63.55        27.85        13.45       185.79 
TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV 
       16.73        19.50        18.41        17.36        16.57        51.45 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FH 
       48.43        11.87        52.54        96.30        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 
       29.65        41.06        18.61        20.19        35.21        63.68 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.83        56.58        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B 
        9.57        20.02        20.12        11.31        34.98        31.76 
TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       24.99        13.18        10.03        24.33        85.55        78.21 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        72.72        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        83.64        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
        4.87        23.93         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B 
        1.91         3.68        29.33        32.58        15.72        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V 
       37.51        36.79        29.92        33.63        10.65         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.08        26.37        10.22         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
       15.06         1.05         3.95        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
        2.20       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A2P8 
       16.31        39.29        36.62        31.10        23.38         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       45.57        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW 
       46.26        57.60        50.73        35.15        38.07        16.34 
TCGA-EO-A3KX TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       38.47        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 
       33.34        18.84        16.11        32.78        11.08        12.59 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       45.76        31.04        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A3PX 
       39.88        77.33        25.22        59.01        30.67        78.38 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64         4.44        20.75        18.28         0.23 

  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                          0.07                           0.23 
  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                        225.50                         185.79 
  AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE 
                        27.350                         30.555 
[1] "0.1 - 225.5 (27.4)" "0.2 - 185.8 (30.6)"
[1] "hr=" "2.2"
D20V2, binary
                                cls
clus                               0   1
  AMP PEAK 20(8Q24.21) MUTATED   111  83
  AMP PEAK 20(8Q24.21) WILD-TYPE 179 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(8Q24.21) MUTATED    111   83
  AMP PEAK 20(8Q24.21) WILD-TYPE  179  141
     clus
vv    AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE
  NO                           111                            179
  YES                           83                            141
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 20(8Q24.21) MUTATED                                       118
  AMP PEAK 20(8Q24.21) WILD-TYPE                                     286
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 20(8Q24.21) MUTATED                              11
  AMP PEAK 20(8Q24.21) WILD-TYPE                            11
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 20(8Q24.21) MUTATED                                  80
  AMP PEAK 20(8Q24.21) WILD-TYPE                                33
D20V3, multiclass
                                         clus
vv                                        AMP PEAK 20(8Q24.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          118
  MIXED SEROUS AND ENDOMETRIOID                                     11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 80
                                         clus
vv                                        AMP PEAK 20(8Q24.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            286
  MIXED SEROUS AND ENDOMETRIOID                                       11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(8Q24.21) MUTATED   140   6  10  17
  AMP PEAK 20(8Q24.21) WILD-TYPE 231  16   6  23
D20V4, multiclass
    clus
vv   AMP PEAK 20(8Q24.21) MUTATED AMP PEAK 20(8Q24.21) WILD-TYPE
  R0                          140                            231
  R1                            6                             16
  R2                           10                              6
  RX                           17                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(8Q24.21) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(8Q24.21) MUTATED   160  53
  AMP PEAK 21(8Q24.21) WILD-TYPE 287  37
  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                           213                            324 
  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                            53                             37 
$`AMP PEAK 21(8Q24.21) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A3G3 
       41.06        20.81        10.19        93.99        23.05         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A102 
       80.38        22.06        66.41        12.56         1.81         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
       47.84        33.30        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE 
       17.92        19.89         5.88        39.52        37.02       105.37 
TCGA-A5-A0GJ TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       65.75        23.21        17.59        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M 
      118.19        28.64        25.51        14.96        18.41        20.25 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       21.14        19.79        35.15        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       33.90         1.64        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW 
       21.21        15.62        14.76        16.87        16.87         0.13 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       21.99        63.91        45.53        48.79       125.42       117.99 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E0 TCGA-AP-A3K1 
       97.71        33.40        31.30        46.78        60.23        21.90 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
        0.56        37.78        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H4 
       25.91        76.83        85.48        80.25         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO 
       71.24        40.80        81.37        34.32         2.96        64.93 
TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.20        43.82         0.20        20.52         0.30         0.30 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11I 
        0.39        55.30        57.76        59.84        88.34        75.72 
TCGA-B5-A11L TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR 
       73.64        32.09        77.23        73.28        19.56       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
      102.31        50.89        14.70        31.36       136.60        39.35 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       29.65        34.13        34.95        19.33        20.94        71.24 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MT TCGA-BG-A187 TCGA-BG-A18C 
       74.63        10.72        48.56        21.17        14.73        15.45 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       23.70        22.39        35.90        35.90        35.08        31.00 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TE TCGA-BS-A0TG 
       24.13        16.64        46.95        24.33         4.80        77.95 
TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZZ 
       92.88        73.25        86.99        29.95        28.67        22.55 
TCGA-D1-A15V TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16I 
       39.48        29.33         0.66        36.10        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17R TCGA-D1-A17U 
       31.07         0.69        18.67        14.73        11.15        22.92 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       13.22         0.72         2.07        48.79         8.48        58.95 
TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       18.84        71.61       109.08        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       12.39       110.10        79.10        58.95        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       37.71        66.90        51.52        51.42        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        22.26        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS 
       54.15        23.90        32.71        19.27        17.62        22.03 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.81        37.05        19.33        22.82        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX 
       27.35        32.52        11.38         7.99        96.69         9.34 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        59.28        41.56         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 
       13.28         9.47        26.10        18.21        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A744 TCGA-SL-A6J9 
        8.19        14.83         0.07 

$`AMP PEAK 21(8Q24.21) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        95.47        67.66        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
       61.18        27.88        27.09        61.87        51.55        14.27 
TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-FI-A2CX TCGA-FI-A2D5 
       19.79        16.93         6.21        22.78        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00        23.74         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG 
      149.56        83.51        17.85        32.78       112.54       123.68 
TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       54.02        68.65        37.91        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       42.35        15.95        31.99        66.15        24.72        34.95 
TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QO TCGA-AJ-A3EK TCGA-AJ-A3EL 
       11.21        14.43        10.26        34.36        14.66        22.49 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.35        15.95        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
       35.11       129.80        23.31        86.07        48.03        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       23.87        12.62        20.91       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
       49.15         6.71        45.86        27.85        51.12        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CN 
       77.39        13.28        32.91        34.09        73.41        37.58 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        38.24        17.75        30.74        31.13         0.23 
TCGA-AX-A3FW TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.56         0.26         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       86.37        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        27.29        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11N 
       27.85        13.45       185.79       113.36        54.44        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       85.78        52.04        16.73        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA 
       16.57        51.45        48.43        11.87        52.54        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       93.50        71.84        27.65        41.06        18.61        20.19 
TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       35.21        63.68        41.52        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       59.74        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A18A 
       52.64        52.83        56.58        14.83        13.78        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA 
       15.45         9.57        20.02        20.12        11.31        34.98 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TC 
       31.76        24.99        13.18        10.03         9.86        85.55 
TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 
      114.90        85.84        82.39        81.57        72.72        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       89.59        63.58        83.64        66.48        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        0.56         4.87        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B 
       29.88         1.91         3.68        32.58        15.72        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        33.63        10.65 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33         1.41        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
       15.06         1.05         3.95        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
        2.20       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A2P8 
       16.31        39.29        36.62        31.10        23.38         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       45.57        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW 
       46.26        57.60        50.73        35.15        38.07        16.34 
TCGA-EO-A3KX TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       38.47        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 
       33.34        18.84        16.11        32.78        11.08        12.59 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       45.76        31.04        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A3PX 
       39.88        77.33        25.22        59.01        30.67        78.38 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64         4.44        20.75        18.28         0.23 

  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                          0.07                           0.23 
  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                        225.50                         185.79 
  AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE 
                         27.16                          30.74 
[1] "0.1 - 225.5 (27.2)" "0.2 - 185.8 (30.7)"
[1] "hr=" "2.4"
D21V2, binary
                                cls
clus                               0   1
  AMP PEAK 21(8Q24.21) MUTATED   114  86
  AMP PEAK 21(8Q24.21) WILD-TYPE 176 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(8Q24.21) MUTATED    114   86
  AMP PEAK 21(8Q24.21) WILD-TYPE  176  138
     clus
vv    AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE
  NO                           114                            176
  YES                           86                            138
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 21(8Q24.21) MUTATED                                       121
  AMP PEAK 21(8Q24.21) WILD-TYPE                                     283
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 21(8Q24.21) MUTATED                              10
  AMP PEAK 21(8Q24.21) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 21(8Q24.21) MUTATED                                  84
  AMP PEAK 21(8Q24.21) WILD-TYPE                                29
D21V3, multiclass
                                         clus
vv                                        AMP PEAK 21(8Q24.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          121
  MIXED SEROUS AND ENDOMETRIOID                                     10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 84
                                         clus
vv                                        AMP PEAK 21(8Q24.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            283
  MIXED SEROUS AND ENDOMETRIOID                                       12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(8Q24.21) MUTATED   145   6  12  16
  AMP PEAK 21(8Q24.21) WILD-TYPE 226  16   4  24
D21V4, multiclass
    clus
vv   AMP PEAK 21(8Q24.21) MUTATED AMP PEAK 21(8Q24.21) WILD-TYPE
  R0                          145                            226
  R1                            6                             16
  R2                           12                              4
  RX                           16                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(9P24.2) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 22(9P24.2) MUTATED    46  18
  AMP PEAK 22(9P24.2) WILD-TYPE 401  72
  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                           64                           473 
  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                           18                            72 
$`AMP PEAK 22(9P24.2) MUTATED`
TCGA-AJ-A2QM TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       29.39        67.66        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-E6-A8L9 TCGA-EY-A212 TCGA-KP-A3VZ 
       80.38        22.06        12.56        33.30        10.19        23.74 
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A3EM 
       37.02        31.99       118.19        14.96        21.14        22.26 
TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A5FX TCGA-AX-A05Z TCGA-AX-A06F TCGA-AX-A0IU 
       36.89       125.42        36.13        71.51        57.47        35.74 
TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11H 
       30.12         2.96        20.52         0.39        27.29        88.34 
TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       75.72        11.87        29.65        22.39        35.08        24.13 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A2G7 
       61.87        92.88        31.07        14.73         0.72        58.95 
TCGA-DF-A2KS TCGA-DI-A2QU TCGA-E6-A1M0 TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A3KW 
      109.08        31.10        58.95        37.71        57.60        16.34 
TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OQ 
       54.15        17.62        22.03        11.08        20.05        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       32.52        11.38        96.69        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-PG-A7D5 TCGA-PG-A914 TCGA-SL-A6J9 
        1.74        38.70        22.59         0.07 

$`AMP PEAK 22(9P24.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       20.81        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       12.26        36.39        27.09        66.41        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
        6.21        22.78        17.88        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
        0.43        39.52        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       11.21        18.41        20.25        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       35.15        34.36        34.16        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        45.53        23.87        12.62        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        51.12        21.90         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW 
       49.87        27.39        30.02        60.66        61.08        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       25.51        26.37        32.02        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       72.62        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
       59.84       185.79       113.36        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       77.95        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       11.51        29.92        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.95        48.79         8.48        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       17.29         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39       110.10        23.38        79.10 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y 
       49.15        61.74        61.55        66.90        46.26        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        46.42        26.96        22.26        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT 
       23.90        33.34        32.71        19.27        18.84        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       32.78        15.81        37.05        19.33        12.59        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       45.76        31.04        27.35        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       68.38        39.88        77.33         7.99        25.22        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
        9.34        28.93        30.67        17.75        14.04        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 
        9.47        26.10        18.21        23.24        21.30         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                       125.42                        225.50 
  AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE 
                       30.595                        29.880 
[1] "0.1 - 125.4 (30.6)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.8"
D22V2, binary
                               cls
clus                              0   1
  AMP PEAK 22(9P24.2) MUTATED    35  22
  AMP PEAK 22(9P24.2) WILD-TYPE 255 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(9P24.2) MUTATED     35   22
  AMP PEAK 22(9P24.2) WILD-TYPE  255  202
     clus
vv    AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE
  NO                           35                           255
  YES                          22                           202
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 22(9P24.2) MUTATED                                        26
  AMP PEAK 22(9P24.2) WILD-TYPE                                     378
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 22(9P24.2) MUTATED                               3
  AMP PEAK 22(9P24.2) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 22(9P24.2) MUTATED                                  36
  AMP PEAK 22(9P24.2) WILD-TYPE                                77
D22V3, multiclass
                                         clus
vv                                        AMP PEAK 22(9P24.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          26
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                36
                                         clus
vv                                        AMP PEAK 22(9P24.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           378
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 22(9P24.2) MUTATED    39   3   3   9
  AMP PEAK 22(9P24.2) WILD-TYPE 332  19  13  31
D22V4, multiclass
    clus
vv   AMP PEAK 22(9P24.2) MUTATED AMP PEAK 22(9P24.2) WILD-TYPE
  R0                          39                           332
  R1                           3                            19
  R2                           3                            13
  RX                           9                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(9Q34.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 23(9Q34.3) MUTATED    28  11
  AMP PEAK 23(9Q34.3) WILD-TYPE 419  79
  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                           39                           498 
  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                           11                            79 
$`AMP PEAK 23(9Q34.3) MUTATED`
TCGA-AJ-A2QM TCGA-AP-A05D TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-EY-A212 TCGA-EY-A547 
       29.39        57.80         1.38        27.09        10.19        17.92 
TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A1OH TCGA-A5-A7WK TCGA-AJ-A3EJ TCGA-AP-A052 
       60.53        28.27        36.33        18.41         1.64        21.99 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0LH TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A2H5 
       63.91        36.89        36.36         0.56        35.74        71.24 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G7 TCGA-B5-A0K3 TCGA-B5-A1N2 TCGA-B5-A5OD 
        2.96        64.93         0.30        27.29        31.36        34.13 
TCGA-BK-A139 TCGA-D1-A16I TCGA-D1-A1NX TCGA-E6-A1M0 TCGA-EO-A2CG TCGA-EY-A1GJ 
       31.00        11.51        18.25        58.95        51.42        23.90 
TCGA-EY-A1GS TCGA-EY-A210 TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A7D5 
       22.03        12.59        68.38        59.28         1.74        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       22.59         8.19         0.07 

$`AMP PEAK 23(9Q34.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN 
       12.26        36.39        23.05        61.18        27.88        80.38 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       22.06        66.41        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
        6.21        22.78        17.88        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
        5.88        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GV 
       74.10        65.75        46.55        73.87        36.82        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       19.79        35.15        34.36        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       33.90        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11         0.13       129.80        23.31        86.07        48.03 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       45.53        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        21.90        36.13        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       30.12        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       17.75        30.74        31.13         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 
       43.82         0.20        20.52         0.30         0.26         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        11.87        52.54       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
       22.39        35.90        34.98        35.90        35.08        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22         0.72        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
       15.88         4.27        18.84        17.29         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 
       12.39        31.10       110.10        23.38        79.10         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        32.52        11.38        14.14        14.70        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
        9.34        28.93        30.67        41.56        78.38        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       14.04        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       21.30        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                        71.24                        225.50 
  AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE 
                        27.29                         30.05 
[1] "0.1 - 71.2 (27.3)"  "0.1 - 225.5 (30.0)"
[1] "hr=" "2.3"
D23V2, binary
                               cls
clus                              0   1
  AMP PEAK 23(9Q34.3) MUTATED    19  16
  AMP PEAK 23(9Q34.3) WILD-TYPE 271 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 23(9Q34.3) MUTATED     19   16
  AMP PEAK 23(9Q34.3) WILD-TYPE  271  208
     clus
vv    AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE
  NO                           19                           271
  YES                          16                           208
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 23(9Q34.3) MUTATED                                        13
  AMP PEAK 23(9Q34.3) WILD-TYPE                                     391
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 23(9Q34.3) MUTATED                               5
  AMP PEAK 23(9Q34.3) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 23(9Q34.3) MUTATED                                  21
  AMP PEAK 23(9Q34.3) WILD-TYPE                                92
D23V3, multiclass
                                         clus
vv                                        AMP PEAK 23(9Q34.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          13
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                21
                                         clus
vv                                        AMP PEAK 23(9Q34.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           391
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 23(9Q34.3) MUTATED    27   2   2   1
  AMP PEAK 23(9Q34.3) WILD-TYPE 344  20  14  39
D23V4, multiclass
    clus
vv   AMP PEAK 23(9Q34.3) MUTATED AMP PEAK 23(9Q34.3) WILD-TYPE
  R0                          27                           344
  R1                           2                            20
  R2                           2                            14
  RX                           1                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(10Q22.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(10Q22.2) MUTATED   113  29
  AMP PEAK 24(10Q22.2) WILD-TYPE 334  61
  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                           142                            395 
  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                            29                             61 
$`AMP PEAK 24(10Q22.2) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AX-A06D TCGA-BG-A0M6 TCGA-BG-A0MS 
       29.39        10.19       110.63        12.26        22.06        61.87 
TCGA-BG-A0VT TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GQ TCGA-EY-A214 
       51.55         4.44        47.84         6.21        17.88        14.40 
TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GU 
        5.88        39.52        37.02       105.37        65.75        28.27 
TCGA-A5-A0GV TCGA-A5-A0R9 TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-AJ-A23M 
       54.02        24.62        36.33        33.07       118.19        20.25 
TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3QS 
       10.26        18.90         1.64        17.06        36.99        16.87 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LI 
       63.91        36.89        20.91        48.79       117.99        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
       46.72        82.52        80.78        27.85        51.12        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A06J TCGA-AX-A0IU TCGA-AX-A0IW 
       33.21        29.69        80.55        30.02        35.74        37.78 
TCGA-AX-A1C4 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CJ TCGA-AX-A2H2 TCGA-AX-A2HH 
       13.28        32.02        25.91        73.41         4.77        17.75 
TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A11E 
        2.96         0.56        43.82        55.30        27.85        59.84 
TCGA-B5-A11F TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
      185.79        75.72        73.64        32.09        77.23        73.28 
TCGA-B5-A1MV TCGA-B5-A5OD TCGA-BG-A0LX TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0MG 
       51.45        34.13        20.19        20.94        35.21        48.56 
TCGA-BG-A0RY TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A3PP TCGA-BK-A0C9 
       15.42        56.58        14.73        14.01        22.39        35.90 
TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0UV 
       35.08        16.64        46.95        61.87        30.74        73.25 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZU 
       63.58        83.64        66.48        29.95         8.55        28.67 
TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 TCGA-D1-A16N 
       39.48         1.91        29.33         0.66        37.32        31.07 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17T TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DH 
        0.69        18.67         2.33        18.25         2.07        18.84 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1M0 TCGA-E6-A2P9 TCGA-EO-A1Y7 
       35.38         9.37        12.39        58.95        45.57        49.15 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3L0 
       51.52        51.42        19.40        26.96        22.26        51.09 
TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GW 
       54.15        23.34        19.27        22.03        16.11        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       37.05        19.33        12.59        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       27.35         7.99        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A7D5 
       30.67        78.38         1.74        14.04         9.47        38.70 
TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZJ 
        8.19        14.83         4.44        18.28 

$`AMP PEAK 24(10Q22.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A1CP 
       20.81        57.80        93.99        95.47        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       23.05        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A3JP 
       66.41        12.56        14.27         1.81        19.79        16.93 
TCGA-E6-A8L9 TCGA-EY-A1GK TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       33.30        22.78        10.19        18.87        17.92        19.89 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       123.68        74.10        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       36.82        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A2K3 
       29.06        42.35        15.95        31.99        31.99        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       18.41        14.43        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       34.16        18.12        33.90        14.66        22.49        22.26 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LG 
       45.53        23.87        12.62       125.42       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LT 
       36.36        83.97        27.12        33.40        61.64        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A3K1 
       46.78        49.15         6.71        60.23        45.86        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       36.13         0.56        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       79.46        49.87        57.47        27.39        60.66        61.08 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       43.82        40.11        77.39        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN 
       26.37        34.09        76.83        85.48        80.25        37.58 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       38.24        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
       18.35        14.47         0.39        56.91        86.37        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        88.34        54.44        61.68        85.78        52.04 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      225.50       102.31        50.89        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       39.35        27.65        29.65        41.06        34.95        18.61 
TCGA-BG-A0M0 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       19.33        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU 
       51.06        52.01        34.29        52.64        52.83        14.83 
TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       13.78        15.45        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       20.12        11.31        34.98        35.90        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA 
       24.99        24.13        13.18        10.03         9.86        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZR 
       72.72        59.51        89.59        86.99        16.83         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        23.93        22.55         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.88         3.68        32.58        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O 
       37.51        36.79        27.42        11.51        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17U TCGA-D1-A1NS 
        1.51         1.78        11.15        24.30        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22         0.72        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 
       24.30        31.10       110.10        23.38        79.10         2.37 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX 
       35.15        38.07        27.16        46.42        16.34        38.47 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
       14.99        53.88        24.36        27.16        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        32.71        18.84        17.62        32.78        15.81 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       22.82        20.05        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2F9 
       16.96        68.38        39.88        77.33        25.22        59.28 
TCGA-FI-A3PV TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       41.56        17.75        13.28        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
       24.95        23.64        20.75         0.07         0.23 

  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                          0.56                           0.07 
  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                        185.79                         225.50 
  AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE 
                        29.985                         29.880 
[1] "0.6 - 185.8 (30.0)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.3"
D24V2, binary
                                cls
clus                               0   1
  AMP PEAK 24(10Q22.2) MUTATED    81  58
  AMP PEAK 24(10Q22.2) WILD-TYPE 209 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(10Q22.2) MUTATED     81   58
  AMP PEAK 24(10Q22.2) WILD-TYPE  209  166
     clus
vv    AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE
  NO                            81                            209
  YES                           58                            166
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 24(10Q22.2) MUTATED                                        96
  AMP PEAK 24(10Q22.2) WILD-TYPE                                     308
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 24(10Q22.2) MUTATED                               3
  AMP PEAK 24(10Q22.2) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 24(10Q22.2) MUTATED                                  44
  AMP PEAK 24(10Q22.2) WILD-TYPE                                69
D24V3, multiclass
                                         clus
vv                                        AMP PEAK 24(10Q22.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           96
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 24(10Q22.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            308
  MIXED SEROUS AND ENDOMETRIOID                                       19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(10Q22.2) MUTATED   104   6   7   7
  AMP PEAK 24(10Q22.2) WILD-TYPE 267  16   9  33
D24V4, multiclass
    clus
vv   AMP PEAK 24(10Q22.2) MUTATED AMP PEAK 24(10Q22.2) WILD-TYPE
  R0                          104                            267
  R1                            6                             16
  R2                            7                              9
  RX                            7                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(11P11.2) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 25(11P11.2) MUTATED    34  18
  AMP PEAK 25(11P11.2) WILD-TYPE 413  72
  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                            52                            485 
  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                            18                             72 
$`AMP PEAK 25(11P11.2) MUTATED`
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-BG-A0VT 
       20.81       110.63        27.88         1.38        66.41        51.55 
TCGA-EY-A212 TCGA-EY-A72D TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3EM TCGA-AJ-A3TW 
       10.19         5.88        25.51        14.43        22.26        16.87 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW 
       45.53        48.79        46.78        36.13        35.74        37.78 
TCGA-AX-A1C9 TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-B5-A0JT TCGA-B5-A0K4 
       26.37         4.77        30.12         2.96        55.30        57.76 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M2 TCGA-BG-A18C 
       50.89        11.87        29.65        34.95        20.94        15.45 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 
       22.39        35.08        92.88        83.64        22.55        37.32 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QY 
       11.51        18.67        14.73        25.91        35.38       110.10 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EY-A1GM TCGA-EY-A210 TCGA-FI-A3PX TCGA-H5-A2HR 
       37.71        51.42        32.71        12.59        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A915 
       17.75        14.04        26.10         8.19 

$`AMP PEAK 25(11P11.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        10.19        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-B5-A0JN TCGA-B5-A0KB 
       12.26        36.39        23.05        61.18        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       22.06        61.87        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX 
       17.88        14.40        18.87        17.92        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH 
       29.06        42.35        15.95        31.99        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
       14.96        11.21        18.41        20.25        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       19.79        35.15        34.36        34.16        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       33.90         1.64        14.66        22.49        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       63.91        36.89        23.87        12.62        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        21.90         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       25.51        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        38.24        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47         0.39        56.91        86.37        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       27.29        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      225.50       102.31        51.45        14.70        48.43        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       27.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
       15.88         4.27        18.84        17.29         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
      109.08       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       33.34        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       32.78        15.81        11.08        37.05        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       20.05        45.76        31.04        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       77.33         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W1 
       28.93        30.67        59.28        41.56        13.28         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        21.30        38.70        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                          1.38                           0.07 
  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                        110.63                         225.50 
  AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE 
                        27.125                         30.020 
[1] "1.4 - 110.6 (27.1)" "0.1 - 225.5 (30.0)"
[1] "hr=" "2.5"
D25V2, binary
                                cls
clus                               0   1
  AMP PEAK 25(11P11.2) MUTATED    29  21
  AMP PEAK 25(11P11.2) WILD-TYPE 261 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 25(11P11.2) MUTATED     29   21
  AMP PEAK 25(11P11.2) WILD-TYPE  261  203
     clus
vv    AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE
  NO                            29                            261
  YES                           21                            203
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 25(11P11.2) MUTATED                                        17
  AMP PEAK 25(11P11.2) WILD-TYPE                                     387
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 25(11P11.2) MUTATED                               4
  AMP PEAK 25(11P11.2) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 25(11P11.2) MUTATED                                  31
  AMP PEAK 25(11P11.2) WILD-TYPE                                82
D25V3, multiclass
                                         clus
vv                                        AMP PEAK 25(11P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           17
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 31
                                         clus
vv                                        AMP PEAK 25(11P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            387
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 25(11P11.2) MUTATED    35   1   2   6
  AMP PEAK 25(11P11.2) WILD-TYPE 336  21  14  34
D25V4, multiclass
    clus
vv   AMP PEAK 25(11P11.2) MUTATED AMP PEAK 25(11P11.2) WILD-TYPE
  R0                           35                            336
  R1                            1                             21
  R2                            2                             14
  RX                            6                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(11Q13.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(11Q13.2) MUTATED    54  20
  AMP PEAK 26(11Q13.2) WILD-TYPE 393  70
  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                            74                            463 
  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                            20                             70 
$`AMP PEAK 26(11Q13.2) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       20.81        10.19        67.66        27.88         1.38        80.38 
TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A72D TCGA-5B-A90C 
       66.41        51.55        33.30        10.19         5.88        39.52 
TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A23M 
       65.75        31.99        36.33        25.51        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A5FX 
       14.43        21.14        63.91        36.89        48.79        36.13 
TCGA-AX-A0IW TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H4 
       37.78        32.91        26.37        32.02         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-B5-A0JT 
       71.24         2.96        43.82        20.52         0.30        55.30 
TCGA-B5-A0JX TCGA-B5-A0K4 TCGA-B5-A11Q TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FB 
       58.75        57.76        32.09        50.89        31.36        93.50 
TCGA-B5-A3S1 TCGA-BG-A0M2 TCGA-BG-A0MC TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A4ZD 
       29.65        20.94        41.52        15.45        35.08        16.64 
TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V 
       92.88        29.95        37.32        11.51        18.67         3.95 
TCGA-D1-A17K TCGA-D1-A1O0 TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       28.08         2.07        71.61       109.08        25.91        35.38 
TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A210 
       31.10        49.15        16.34        54.15        23.90        12.59 
TCGA-EY-A2OQ TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W3 
       29.10        68.38         9.34        78.38        14.04        26.10 
TCGA-PG-A914 TCGA-SL-A6J9 
       22.59         0.07 

$`AMP PEAK 26(11Q13.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D 
       18.08       110.63        57.80        93.99        95.47        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS 
       36.39        23.05        61.18        27.09        22.06        61.87 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 
       16.93         6.21        22.78        17.88        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       17.92        19.89        66.77        13.84        73.32        36.00 
TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       23.74         0.43        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
      118.19        66.15        28.64        24.72        34.95        14.96 
TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       11.21        10.26        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N 
       21.99        23.31        86.07        48.03        45.53        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CC 
       40.11        77.39        13.28        34.65        25.51        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.30         0.26         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY 
        0.39        56.91        86.37        59.24        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        27.29        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       52.04        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50       102.31        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        11.87        52.54       136.60        96.30 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       71.84        39.35        27.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       18.61        20.19        19.33        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       74.63        10.72        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31        22.39        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       36.10        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30         9.37        12.39       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       11.08        37.05        19.33        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        39.88        77.33         7.99        25.22        96.69 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       59.01        28.93        30.67        59.28        41.56         1.74 
TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       17.75        13.28         9.47        18.21        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                          0.07                           0.13 
  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                        109.08                         225.50 
  AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE 
                         30.61                          29.69 
[1] "0.1 - 109.1 (30.6)" "0.1 - 225.5 (29.7)"
[1] "hr=" "1.9"
D26V2, binary
                                cls
clus                               0   1
  AMP PEAK 26(11Q13.2) MUTATED    41  29
  AMP PEAK 26(11Q13.2) WILD-TYPE 249 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(11Q13.2) MUTATED     41   29
  AMP PEAK 26(11Q13.2) WILD-TYPE  249  195
     clus
vv    AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE
  NO                            41                            249
  YES                           29                            195
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 26(11Q13.2) MUTATED                                        36
  AMP PEAK 26(11Q13.2) WILD-TYPE                                     368
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 26(11Q13.2) MUTATED                               4
  AMP PEAK 26(11Q13.2) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 26(11Q13.2) MUTATED                                  34
  AMP PEAK 26(11Q13.2) WILD-TYPE                                79
D26V3, multiclass
                                         clus
vv                                        AMP PEAK 26(11Q13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           36
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 34
                                         clus
vv                                        AMP PEAK 26(11Q13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            368
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(11Q13.2) MUTATED    43   2   3  10
  AMP PEAK 26(11Q13.2) WILD-TYPE 328  20  13  30
D26V4, multiclass
    clus
vv   AMP PEAK 26(11Q13.2) MUTATED AMP PEAK 26(11Q13.2) WILD-TYPE
  R0                           43                            328
  R1                            2                             20
  R2                            3                             13
  RX                           10                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(11Q14.1) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(11Q14.1) MUTATED    39  21
  AMP PEAK 27(11Q14.1) WILD-TYPE 408  69
  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                            60                            477 
  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                            21                             69 
$`AMP PEAK 27(11Q14.1) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0VT 
       20.81        10.19         1.38        80.38        66.41        51.55 
TCGA-EY-A212 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LO 
       10.19        39.52        37.02        65.75        36.33        25.51 
TCGA-AJ-A23N TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AP-A5FX TCGA-AX-A0IW 
       14.43        18.12        16.87        48.79        36.13        37.78 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3G1 
       32.02        25.91         4.77        30.12         2.96        20.52 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K4 TCGA-B5-A11Q TCGA-B5-A1MS 
        0.39        55.30        58.75        57.76        32.09       102.31 
TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-BG-A0M2 TCGA-BG-A0MC TCGA-BG-A18C 
       50.89        31.36        39.35        20.94        41.52        15.45 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16V 
       22.39        35.08        16.64        92.88        11.51         3.95 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.25         2.07        71.61       109.08        25.91        35.38 
TCGA-DI-A2QT TCGA-EO-A1Y5 TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A2OQ TCGA-EY-A4KR 
       12.39        10.92        22.26        23.90        29.10        11.38 
TCGA-FI-A2EY TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       28.93        78.38        14.04        22.59         8.19         4.44 

$`AMP PEAK 27(11Q14.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0KB 
       12.26        36.39        23.05        61.18        27.88        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       22.06        61.87        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       17.88        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP 
      112.54       105.37       123.68        74.10        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95        31.99        31.99        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       25.51        26.37        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 
        0.23         0.20         0.56        43.82         0.20         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.26         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       86.37        59.24        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        52.04        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
       16.57       225.50        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       52.54       136.60        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       19.33        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22         0.72        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
       58.95        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30         9.37        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       20.05        45.76        31.04        27.35        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
       25.22        96.69        59.01         9.34        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       41.56         1.74        17.75        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 
       18.21        23.24        21.30        38.70        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                          0.39                           0.07 
  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                        109.08                         225.50 
  AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE 
                         25.91                          30.08 
[1] "0.4 - 109.1 (25.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.9"
D27V2, binary
                                cls
clus                               0   1
  AMP PEAK 27(11Q14.1) MUTATED    32  25
  AMP PEAK 27(11Q14.1) WILD-TYPE 258 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(11Q14.1) MUTATED     32   25
  AMP PEAK 27(11Q14.1) WILD-TYPE  258  199
     clus
vv    AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE
  NO                            32                            258
  YES                           25                            199
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 27(11Q14.1) MUTATED                                        24
  AMP PEAK 27(11Q14.1) WILD-TYPE                                     380
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 27(11Q14.1) MUTATED                               1
  AMP PEAK 27(11Q14.1) WILD-TYPE                            21
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 27(11Q14.1) MUTATED                                  35
  AMP PEAK 27(11Q14.1) WILD-TYPE                                78
D27V3, multiclass
                                         clus
vv                                        AMP PEAK 27(11Q14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           24
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 35
                                         clus
vv                                        AMP PEAK 27(11Q14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            380
  MIXED SEROUS AND ENDOMETRIOID                                       21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(11Q14.1) MUTATED    33   1   3   9
  AMP PEAK 27(11Q14.1) WILD-TYPE 338  21  13  31
D27V4, multiclass
    clus
vv   AMP PEAK 27(11Q14.1) MUTATED AMP PEAK 27(11Q14.1) WILD-TYPE
  R0                           33                            338
  R1                            1                             21
  R2                            3                             13
  RX                            9                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = AMP PEAK 28(12P12.1) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(12P12.1) MUTATED    72  19
  AMP PEAK 28(12P12.1) WILD-TYPE 375  71
  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                            91                            446 
  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                            19                             71 
$`AMP PEAK 28(12P12.1) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 
       41.06        20.81        10.19        23.05        27.88         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
       80.38        22.06        66.41        47.84        16.93        33.30 
TCGA-EY-A214 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GE 
       14.40         5.88        23.74        39.52       149.56       105.37 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BD 
       17.59        31.99        36.33        66.15        20.25        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A1DO TCGA-AP-A1DQ 
       18.12        16.87        20.91       125.42        31.30        46.78 
TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A2H2 
       51.12        80.55        37.78        77.39        32.02         4.77 
TCGA-AX-A2HA TCGA-AX-A2HK TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11R 
       81.37         2.96         0.39        27.29        27.85        77.23 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC 
       19.56        19.50        11.87        31.36        29.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0M2 TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE 
       34.13        20.94        48.56        52.83        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A13B TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V7 
       22.39        31.76         4.80        61.87        92.88        63.58 
TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A17K TCGA-D1-A17U TCGA-D1-A1O0 
       36.10        11.51        33.63        28.08        22.92         2.07 
TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
       18.84        71.61        24.30        35.38       110.10        79.10 
TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GC 
       10.92        51.42        35.15        27.16        26.96        54.15 
TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A3L3 TCGA-FI-A2D2 
       19.27        22.03        19.33        12.59        27.35        77.33 
TCGA-FI-A2D6 TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-PG-A914 
       25.22        28.93        78.38        17.75        14.04        22.59 
TCGA-PG-A915 
        8.19 

$`AMP PEAK 28(12P12.1) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
      110.63        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV 
       36.39        61.18        27.09        61.87        51.55        12.56 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A1G7 TCGA-EY-A1GK 
       14.27         1.81        19.79         4.44         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX 
       17.88        10.19        18.87        17.92        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG 
       37.02        83.51        17.85        32.78       112.54       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        37.91        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
      118.19        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        18.41        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       35.15        34.36        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.62        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        90.97        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       60.23        45.86        27.85        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        33.21        29.69        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
       60.66        61.08        35.74        43.82        40.11        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        34.65        25.51        26.37        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        85.48        73.41        80.25        37.58        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       71.24        40.80        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       36.49        72.62        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S 
       73.64        61.68        85.78        52.04        32.09        73.28 
TCGA-B5-A11U TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       16.73        18.41        17.36        16.57       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        51.45        14.70        48.43        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OE 
       96.30        93.50        71.84        39.35        27.65        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       18.61        20.19        19.33        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       74.63        10.72        41.52        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.01        15.45         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.00        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       24.33        85.55        78.21        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       27.42        29.92        31.07        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       11.15        24.30         2.33         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
       48.79         8.48        58.95        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QT 
       25.91        16.31        39.29        36.62         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       50.73        38.07        46.42        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        23.90        33.34        32.71        18.84        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2OM 
       16.11        32.78        15.81        11.08        37.05        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR 
       20.05        45.76        31.04        29.10        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01         9.34        30.67        59.28        41.56 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        1.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        38.70        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                          0.39                           0.07 
  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                        149.56                         225.50 
  AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE 
                         27.88                          30.10 
[1] "0.4 - 149.6 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.3"
D28V2, binary
                                cls
clus                               0   1
  AMP PEAK 28(12P12.1) MUTATED    43  45
  AMP PEAK 28(12P12.1) WILD-TYPE 247 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(12P12.1) MUTATED     43   45
  AMP PEAK 28(12P12.1) WILD-TYPE  247  179
     clus
vv    AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE
  NO                            43                            247
  YES                           45                            179
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 28(12P12.1) MUTATED                                        44
  AMP PEAK 28(12P12.1) WILD-TYPE                                     360
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 28(12P12.1) MUTATED                               4
  AMP PEAK 28(12P12.1) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 28(12P12.1) MUTATED                                  44
  AMP PEAK 28(12P12.1) WILD-TYPE                                69
D28V3, multiclass
                                         clus
vv                                        AMP PEAK 28(12P12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           44
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 28(12P12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            360
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(12P12.1) MUTATED    64   2   3   5
  AMP PEAK 28(12P12.1) WILD-TYPE 307  20  13  35
D28V4, multiclass
    clus
vv   AMP PEAK 28(12P12.1) MUTATED AMP PEAK 28(12P12.1) WILD-TYPE
  R0                           64                            307
  R1                            2                             20
  R2                            3                             13
  RX                            5                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = AMP PEAK 29(12Q13.11) MUTATION ANALYSIS
D29V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 29(12Q13.11) MUTATED    69  18
  AMP PEAK 29(12Q13.11) WILD-TYPE 378  72
  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                             87                             450 
  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                             18                              72 
$`AMP PEAK 29(12Q13.11) MUTATED`
TCGA-AP-A053 TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-D1-A2G5 
      110.63        23.05        61.18         1.38        66.41        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-KP-A3VZ TCGA-A5-A0G2 TCGA-A5-A0G5 
       16.93        33.30        14.40        23.74       149.56        37.02 
TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M 
      105.37        17.59        31.99        36.33        66.15        20.25 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AP-A05P TCGA-AP-A0L9 
       34.16        18.12        22.26        16.87        20.91       125.42 
TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 
       97.71        31.30        51.12        80.55        37.78        77.39 
TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A2HK TCGA-AX-A3FZ 
       32.02         4.77        30.12        81.37         2.96         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11R TCGA-B5-A11V 
        0.30         0.30         0.39        27.29        77.23        19.56 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0M2 TCGA-BG-A0MG TCGA-BG-A0W1 
       31.36        29.65        41.06        20.94        48.56        52.83 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0V7 
       15.45        23.70        22.39         4.80        92.88        63.58 
TCGA-D1-A0ZP TCGA-D1-A16O TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3JQ 
       29.95        33.63        18.67         2.07        58.95        17.29 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       71.61       109.08        24.30        35.38        12.39       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EY-A1GJ TCGA-EY-A1GM 
       79.10        49.15        51.42        35.15        23.90        32.71 
TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A3L3 TCGA-EY-A4KR 
       19.27        17.62        19.33        12.59        27.35        11.38 
TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A3PX TCGA-K6-A3WQ 
       77.33        25.22        59.01        28.93        78.38        14.04 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-SL-A6J9 
       38.70        22.59         0.07 

$`AMP PEAK 29(12Q13.11) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81        10.19        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB 
       67.66        12.26        36.39        27.88        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       19.79         4.44         6.21        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        37.91        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 
       29.06        42.35        15.95        31.99        33.07       118.19 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.62        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       35.74        43.82        40.11        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       25.51        26.37        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC 
       73.41        80.25        37.58        71.24        40.80        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G6 
        0.23         0.20         0.56        43.82        20.52         0.26 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       73.28        16.73        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       39.35        27.65        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       19.33        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       41.52        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
        9.57        20.02        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        29.92        31.07        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
       13.22         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95        48.79         8.48        15.88         4.27 
TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       18.84         2.20       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QU 
       25.91        16.31        39.29        36.62         9.37        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        50.73 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       38.07        27.16        46.42        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GS 
       27.16        23.34        23.34        33.34        18.84        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A2OM 
       16.11        32.78        15.81        11.08        37.05        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 
       20.05        45.76        31.04        29.10        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2EU 
       14.70        16.96        68.38        39.88         7.99        96.69 
TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
        9.34        30.67        59.28        41.56         1.74        17.75 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        21.30 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                           0.07                            0.13 
  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                         149.56                          225.50 
  AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE 
                         30.120                          29.785 
[1] "0.1 - 149.6 (30.1)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.2"
D29V2, binary
                                 cls
clus                                0   1
  AMP PEAK 29(12Q13.11) MUTATED    39  40
  AMP PEAK 29(12Q13.11) WILD-TYPE 251 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(12Q13.11) MUTATED     39   40
  AMP PEAK 29(12Q13.11) WILD-TYPE  251  184
     clus
vv    AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE
  NO                             39                             251
  YES                            40                             184
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 29(12Q13.11) MUTATED                                        41
  AMP PEAK 29(12Q13.11) WILD-TYPE                                     363
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 29(12Q13.11) MUTATED                               4
  AMP PEAK 29(12Q13.11) WILD-TYPE                            18
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 29(12Q13.11) MUTATED                                  42
  AMP PEAK 29(12Q13.11) WILD-TYPE                                71
D29V3, multiclass
                                         clus
vv                                        AMP PEAK 29(12Q13.11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            41
  MIXED SEROUS AND ENDOMETRIOID                                       4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  42
                                         clus
vv                                        AMP PEAK 29(12Q13.11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             363
  MIXED SEROUS AND ENDOMETRIOID                                        18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 29(12Q13.11) MUTATED    58   2   5   9
  AMP PEAK 29(12Q13.11) WILD-TYPE 313  20  11  31
D29V4, multiclass
    clus
vv   AMP PEAK 29(12Q13.11) MUTATED AMP PEAK 29(12Q13.11) WILD-TYPE
  R0                            58                             313
  R1                             2                              20
  R2                             5                              11
  RX                             9                              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = AMP PEAK 30(12Q13.2) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(12Q13.2) MUTATED    79  20
  AMP PEAK 30(12Q13.2) WILD-TYPE 368  70
  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                            99                            438 
  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                            20                             70 
$`AMP PEAK 30(12Q13.2) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2HF TCGA-BG-A0M8 TCGA-D1-A2G5 
       10.19        93.99        23.05        27.88        66.41        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KJ-A3U4 
       16.93        33.30        14.40         5.88        66.77        36.00 
TCGA-KP-A3VZ TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 
       23.74       149.56        37.02       105.37        36.82        37.91 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD 
       17.59        31.99        66.15        14.96        20.25        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05P 
       18.12        22.26        17.06        21.99        45.53        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW 
      125.42        36.36        31.30        51.12        80.55        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 
       77.39        34.65        25.51        32.02        25.91         4.77 
TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A0K3 
       30.12        81.37         0.56        43.82        20.52        27.29 
TCGA-B5-A0K8 TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       27.85        77.23        19.56        29.65        41.06        34.13 
TCGA-BG-A0M2 TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP 
       20.94        48.56        52.83        15.45        23.70        22.39 
TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A16O TCGA-D1-A16S 
       16.64         4.80        92.88        63.58        33.63        18.67 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1C3 
        2.07        18.84        17.29        71.61       109.08        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       35.38        12.39       110.10        79.10        49.15        37.71 
TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR 
       51.42        35.15        54.15        23.90        19.27        17.62 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2D2 
       19.33        12.59        20.05        27.35        32.52        77.33 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.22        59.01        59.28        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-SL-A6J9 
       14.04        38.70         0.07 

$`AMP PEAK 30(12Q13.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        20.81       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       12.26        36.39        61.18         1.38        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       19.79         4.44         6.21        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       18.87        17.92        19.89        13.84        73.32         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       39.52        10.29       106.88        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      112.54       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       73.87        28.27        54.02        23.21        68.65        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH 
       24.62        29.06        42.35        15.95        31.99        36.33 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07       118.19        28.64        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        18.41        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       35.15        34.36        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ 
       48.79       117.99       110.37        66.25        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        33.21        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE 
       43.82        40.11        13.28        32.91        26.37        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 
       76.83        85.48        73.41        80.25        37.58        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       40.80        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
        2.96        31.13        64.93         0.23         0.20         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W 
       85.78        52.04        32.09        73.28        16.73        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.95        18.61        20.19        19.33        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK 
       63.68        74.63        10.72        41.52        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.73        14.01        15.45         9.57        20.02        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       11.31        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        85.55        78.21        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       31.07        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KU 
        8.48        58.95        15.88         4.27         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62         9.37        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
       45.57        16.04         7.36        16.80        10.92        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       34.39        50.73        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR 
       37.05        22.82        45.76        31.04        29.10        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KP-A3W0 
       96.69         9.34        28.93        30.67        41.56        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
        9.47        26.10        18.21        23.24        21.30        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                          0.07                           0.13 
  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                        149.56                         225.50 
  AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE 
                        31.300                         29.785 
[1] "0.1 - 149.6 (31.3)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.2"
D30V2, binary
                                cls
clus                               0   1
  AMP PEAK 30(12Q13.2) MUTATED    55  39
  AMP PEAK 30(12Q13.2) WILD-TYPE 235 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(12Q13.2) MUTATED     55   39
  AMP PEAK 30(12Q13.2) WILD-TYPE  235  185
     clus
vv    AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE
  NO                            55                            235
  YES                           39                            185
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 30(12Q13.2) MUTATED                                        51
  AMP PEAK 30(12Q13.2) WILD-TYPE                                     353
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 30(12Q13.2) MUTATED                               4
  AMP PEAK 30(12Q13.2) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 30(12Q13.2) MUTATED                                  45
  AMP PEAK 30(12Q13.2) WILD-TYPE                                68
D30V3, multiclass
                                         clus
vv                                        AMP PEAK 30(12Q13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           51
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 45
                                         clus
vv                                        AMP PEAK 30(12Q13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            353
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 30(12Q13.2) MUTATED    70   3   7   7
  AMP PEAK 30(12Q13.2) WILD-TYPE 301  19   9  33
D30V4, multiclass
    clus
vv   AMP PEAK 30(12Q13.2) MUTATED AMP PEAK 30(12Q13.2) WILD-TYPE
  R0                           70                            301
  R1                            3                             19
  R2                            7                              9
  RX                            7                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = AMP PEAK 31(13Q34) MUTATION ANALYSIS
D31V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 31(13Q34) MUTATED    44  14
  AMP PEAK 31(13Q34) WILD-TYPE 403  76
  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                          58                          479 
  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                          14                           76 
$`AMP PEAK 31(13Q34) MUTATED`
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN 
       20.81        93.99        23.05        27.88         1.38        80.38 
TCGA-EY-A214 TCGA-KP-A3VZ TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 
       14.40        23.74        37.02        31.99        36.33        28.64 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A1DV 
       20.25        14.43        16.87        48.79       125.42         6.71 
TCGA-AW-A1PO TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2IO TCGA-B5-A0K8 
        0.56        32.02         4.77        71.24        64.93        27.85 
TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BK-A26L TCGA-BS-A0TA 
       75.72       102.31        29.65        34.13        24.13        24.33 
TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NW 
       83.64        39.48         0.66        11.51        18.67         0.72 
TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A3JQ TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
       16.87         2.07        17.29        35.38       110.10        79.10 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EY-A1GO 
       10.92        51.52        51.42        19.40        26.96        19.27 
TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 
       22.03        12.59        27.35        11.38        14.70        77.33 
TCGA-FI-A2F9 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       59.28        38.70        22.59         8.19 

$`AMP PEAK 31(13Q34) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        10.19       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       12.26        36.39        61.18        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       17.88        10.19        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C 
       66.77        13.84        73.32        36.00         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       42.35        15.95        31.99        33.07       118.19        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07        48.03        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.62        20.91       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        30.12        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       27.29        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       31.36       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       27.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31        22.39        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       35.08        31.00        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
       10.03         9.86        46.95        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
        1.91         3.68        29.33        32.58        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR 
       58.95        15.88         4.27        18.84         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT 
       16.31        39.29        36.62        24.30         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       66.90        46.26        57.60        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       38.07        27.16        46.42        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        32.71        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       32.52        14.14        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       25.22        96.69        59.01         9.34        28.93        30.67 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       41.56        78.38         1.74        17.75        14.04        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 
        9.47        26.10        18.21        23.24        21.30        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                        0.56                         0.07 
  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                      125.42                       225.50 
  AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE 
                      25.645                       30.150 
[1] "0.6 - 125.4 (25.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.7"
D31V2, binary
                              cls
clus                             0   1
  AMP PEAK 31(13Q34) MUTATED    22  34
  AMP PEAK 31(13Q34) WILD-TYPE 268 190
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 31(13Q34) MUTATED     22   34
  AMP PEAK 31(13Q34) WILD-TYPE  268  190
     clus
vv    AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE
  NO                          22                          268
  YES                         34                          190
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 31(13Q34) MUTATED                                        14
  AMP PEAK 31(13Q34) WILD-TYPE                                     390
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 31(13Q34) MUTATED                               4
  AMP PEAK 31(13Q34) WILD-TYPE                            18
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 31(13Q34) MUTATED                                  40
  AMP PEAK 31(13Q34) WILD-TYPE                                73
D31V3, multiclass
                                         clus
vv                                        AMP PEAK 31(13Q34) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         14
  MIXED SEROUS AND ENDOMETRIOID                                    4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               40
                                         clus
vv                                        AMP PEAK 31(13Q34) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          390
  MIXED SEROUS AND ENDOMETRIOID                                     18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 31(13Q34) MUTATED    35   6   4   6
  AMP PEAK 31(13Q34) WILD-TYPE 336  16  12  34
D31V4, multiclass
    clus
vv   AMP PEAK 31(13Q34) MUTATED AMP PEAK 31(13Q34) WILD-TYPE
  R0                         35                          336
  R1                          6                           16
  R2                          4                           12
  RX                          6                           34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = AMP PEAK 32(14Q24.3) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(14Q24.3) MUTATED    43  21
  AMP PEAK 32(14Q24.3) WILD-TYPE 404  69
  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                            64                            473 
  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                            21                             69 
$`AMP PEAK 32(14Q24.3) MUTATED`
TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AX-A1CR TCGA-AX-A2HF 
       30.15        16.83        20.81       110.63        23.05        27.88 
TCGA-D1-A2G5 TCGA-EY-A212 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GR TCGA-A5-A1OH 
       47.84        10.19        23.74        39.52        36.82        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF 
      118.19        28.64        14.96         1.64        22.26        21.21 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       63.91        36.89       125.42        97.71        46.78        21.90 
TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3GI 
       37.78        25.91        30.12        64.93        43.82         0.39 
TCGA-B5-A0JR TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-BG-A18C TCGA-BG-A3PP 
       56.91        27.29        57.76        50.89        15.45        22.39 
TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A169 
       35.90        24.13        16.64        92.88        22.55        37.32 
TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-DI-A2QY TCGA-E6-A1M0 
       11.51        14.73        18.25         2.07       110.10        58.95 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A4KR 
       10.92        51.52        26.96        54.15        11.08        11.38 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV 
       77.33        59.01         9.34        28.93        59.28        41.56 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A7D5 
       14.04        13.28        18.21        38.70 

$`AMP PEAK 32(14Q24.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3NH 
       41.06        88.18        60.53        29.39        18.08        10.19 
TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       57.80        93.99        95.47        67.66        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       61.18         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       73.87        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       31.99        31.99        33.07        66.15        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       25.51        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       18.90        33.90        14.66        22.49        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       45.53        23.87        12.62        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 
       31.13         0.23         0.20         0.56         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 
       71.44        48.59        36.49        72.62        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50       102.31        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       11.31        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.99        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22         0.72        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        4.27        18.84        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        79.10         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       45.76        31.04        29.10        27.35        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.70        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W1 
       96.69        30.67        78.38         1.74        17.75         9.47 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       26.10        23.24        21.30        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                          0.39                           0.07 
  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                        125.42                         225.50 
  AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE 
                        28.785                         29.950 
[1] "0.4 - 125.4 (28.8)" "0.1 - 225.5 (29.9)"
[1] "hr=" "2.1"
D32V2, binary
                                cls
clus                               0   1
  AMP PEAK 32(14Q24.3) MUTATED    38  23
  AMP PEAK 32(14Q24.3) WILD-TYPE 252 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(14Q24.3) MUTATED     38   23
  AMP PEAK 32(14Q24.3) WILD-TYPE  252  201
     clus
vv    AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE
  NO                            38                            252
  YES                           23                            201
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 32(14Q24.3) MUTATED                                        22
  AMP PEAK 32(14Q24.3) WILD-TYPE                                     382
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 32(14Q24.3) MUTATED                               4
  AMP PEAK 32(14Q24.3) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 32(14Q24.3) MUTATED                                  38
  AMP PEAK 32(14Q24.3) WILD-TYPE                                75
D32V3, multiclass
                                         clus
vv                                        AMP PEAK 32(14Q24.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           22
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        AMP PEAK 32(14Q24.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            382
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(14Q24.3) MUTATED    43   4   2   7
  AMP PEAK 32(14Q24.3) WILD-TYPE 328  18  14  33
D32V4, multiclass
    clus
vv   AMP PEAK 32(14Q24.3) MUTATED AMP PEAK 32(14Q24.3) WILD-TYPE
  R0                           43                            328
  R1                            4                             18
  R2                            2                             14
  RX                            7                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = AMP PEAK 33(14Q32.33) MUTATION ANALYSIS
D33V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 33(14Q32.33) MUTATED    54  24
  AMP PEAK 33(14Q32.33) WILD-TYPE 393  66
  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                             78                             459 
  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                             24                              66 
$`AMP PEAK 33(14Q32.33) MUTATED`
TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3IA TCGA-AX-A1CR TCGA-B5-A0JN TCGA-B5-A0KB 
       30.15        16.83        20.81        23.05        80.38        27.09 
TCGA-BG-A0M8 TCGA-D1-A2G5 TCGA-EY-A212 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR 
       66.41        47.84        10.19        37.02        65.75        36.82 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A3BF TCGA-AJ-A3EM 
       36.33       118.19        28.64        14.96        18.12        22.26 
TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX 
       16.87        63.91        48.79        97.71        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A3FX 
        0.56        37.78        25.91        76.83        30.12        43.82 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A3FD 
        0.26         0.39        56.91        57.76        50.89        39.35 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD 
       34.95        15.45        22.39        35.90        24.13        16.64 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S 
       92.88        83.64        22.55        37.32        11.51        18.67 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A2QY 
        2.07        58.95         4.27        71.61        25.91       110.10 
TCGA-E6-A1M0 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC 
       58.95        49.15        37.71        51.52        26.96        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A4KR 
       23.90        11.08        12.59        20.05        27.35        11.38 
TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV 
       14.70        77.33        59.01         9.34        28.93        41.56 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A914 
        1.74        17.75        14.04        13.28        18.21        22.59 

$`AMP PEAK 33(14Q32.33) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-AJ-A2QM TCGA-AJ-A3BG TCGA-AJ-A3NH 
       41.06        88.18        60.53        29.39        18.08        10.19 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
      110.63        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0MS 
       36.39        61.18        27.88         1.38        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 
       16.93        33.30         6.21        22.78        17.88        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       31.99        33.07        66.15        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        48.03        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        12.62        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       32.02        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.23         0.20         0.56         0.20        20.52         0.30 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JT 
        0.30         1.18        18.35        14.47        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       36.49        72.62        27.29        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       93.50        71.84        27.65        29.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       14.83        13.78        14.73        14.01        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB 
       20.02        23.70        20.12        11.31        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       35.08        31.00        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS 
        8.48        15.88        18.84        17.29         2.20       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        79.10         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        10.92        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.42        19.40        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       38.07        27.16        46.42        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        15.81        37.05        19.33 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 
       22.82        45.76        31.04        29.10        32.52        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        68.38        39.88         7.99        25.22        96.69 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC 
       30.67        59.28        78.38         9.47        26.10        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       21.30        38.70         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                           0.26                            0.07 
  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                         118.19                          225.50 
  AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE 
                         27.995                          30.020 
[1] "0.3 - 118.2 (28.0)" "0.1 - 225.5 (30.0)"
[1] "hr=" "2.2"
D33V2, binary
                                 cls
clus                                0   1
  AMP PEAK 33(14Q32.33) MUTATED    43  31
  AMP PEAK 33(14Q32.33) WILD-TYPE 247 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 33(14Q32.33) MUTATED     43   31
  AMP PEAK 33(14Q32.33) WILD-TYPE  247  193
     clus
vv    AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE
  NO                             43                             247
  YES                            31                             193
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 33(14Q32.33) MUTATED                                        33
  AMP PEAK 33(14Q32.33) WILD-TYPE                                     371
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 33(14Q32.33) MUTATED                               5
  AMP PEAK 33(14Q32.33) WILD-TYPE                            17
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 33(14Q32.33) MUTATED                                  41
  AMP PEAK 33(14Q32.33) WILD-TYPE                                72
D33V3, multiclass
                                         clus
vv                                        AMP PEAK 33(14Q32.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            33
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  41
                                         clus
vv                                        AMP PEAK 33(14Q32.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             371
  MIXED SEROUS AND ENDOMETRIOID                                        17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 33(14Q32.33) MUTATED    50   4   4   9
  AMP PEAK 33(14Q32.33) WILD-TYPE 321  18  12  31
D33V4, multiclass
    clus
vv   AMP PEAK 33(14Q32.33) MUTATED AMP PEAK 33(14Q32.33) WILD-TYPE
  R0                            50                             321
  R1                             4                              18
  R2                             4                              12
  RX                             9                              31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = AMP PEAK 34(15Q26.3) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 34(15Q26.3) MUTATED    26  12
  AMP PEAK 34(15Q26.3) WILD-TYPE 421  78
  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                            38                            499 
  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                            12                             78 
$`AMP PEAK 34(15Q26.3) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-BG-A0M8 
       20.81        10.19        23.05        61.18        27.88        66.41 
TCGA-D1-A102 TCGA-EY-A72D TCGA-FI-A2CX TCGA-AJ-A3BD TCGA-AP-A0LI TCGA-AP-A1DQ 
        4.44         5.88        66.77        34.16        97.71        46.78 
TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2HD TCGA-AX-A3FX TCGA-AX-A3G1 
       34.65        76.83        30.12        46.49        43.82        20.52 
TCGA-B5-A11I TCGA-BK-A0CC TCGA-BS-A0TE TCGA-D1-A16G TCGA-D1-A17K TCGA-DF-A2KS 
       75.72        35.08         4.80        27.42        28.08       109.08 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EY-A1GC 
       35.38       110.10        58.95        51.42        34.39        54.15 
TCGA-EY-A1GW TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A5BC 
       11.08        28.93        41.56        78.38         1.74        23.24 
TCGA-PG-A914 TCGA-QS-A8F1 
       22.59         4.44 

$`AMP PEAK 34(15Q26.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 
       12.26        36.39         1.38        80.38        27.09        22.06 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2D5 
       10.19        14.40        18.87        17.92        19.89        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       73.32        36.00        23.74         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI 
       21.14        19.79        35.15        34.36        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       34.32        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 
       64.93         0.23         0.20         0.56         0.20         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
       18.84        17.29         2.20        71.61       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       24.30         9.37        12.39        31.10        23.38        79.10 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        19.40        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       29.10        27.35        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-JU-AAVI 
       96.69        59.01         9.34        30.67        59.28        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       14.04        13.28         9.47        26.10        18.21        21.30 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                          1.74                           0.07 
  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                         110.1                          225.5 
  AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE 
                         34.52                          29.65 
[1] "1.7 - 110.1 (34.5)" "0.1 - 225.5 (29.6)"
[1] "hr=" "1.8"
D34V2, binary
                                cls
clus                               0   1
  AMP PEAK 34(15Q26.3) MUTATED    25  11
  AMP PEAK 34(15Q26.3) WILD-TYPE 265 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(15Q26.3) MUTATED     25   11
  AMP PEAK 34(15Q26.3) WILD-TYPE  265  213
     clus
vv    AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE
  NO                            25                            265
  YES                           11                            213
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 34(15Q26.3) MUTATED                                        18
  AMP PEAK 34(15Q26.3) WILD-TYPE                                     386
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 34(15Q26.3) MUTATED                               1
  AMP PEAK 34(15Q26.3) WILD-TYPE                            21
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 34(15Q26.3) MUTATED                                  19
  AMP PEAK 34(15Q26.3) WILD-TYPE                                94
D34V3, multiclass
                                         clus
vv                                        AMP PEAK 34(15Q26.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           18
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 19
                                         clus
vv                                        AMP PEAK 34(15Q26.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            386
  MIXED SEROUS AND ENDOMETRIOID                                       21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 34(15Q26.3) MUTATED    20   3   4   5
  AMP PEAK 34(15Q26.3) WILD-TYPE 351  19  12  35
D34V4, multiclass
    clus
vv   AMP PEAK 34(15Q26.3) MUTATED AMP PEAK 34(15Q26.3) WILD-TYPE
  R0                           20                            351
  R1                            3                             19
  R2                            4                             12
  RX                            5                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = AMP PEAK 35(16P11.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 35(16P11.2) MUTATED    49  17
  AMP PEAK 35(16P11.2) WILD-TYPE 398  73
  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                            66                            471 
  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                            17                             73 
$`AMP PEAK 35(16P11.2) MUTATED`
TCGA-AP-A05D TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-D1-A102 
       57.80        80.38        22.06        66.41        51.55         4.44 
TCGA-EY-A212 TCGA-EY-A547 TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A1OG 
       10.19        17.92         5.88        39.52        65.75        31.99 
TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AP-A052 TCGA-AP-A05J 
      118.19        14.96        14.43        34.16        21.99        36.89 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA 
       46.78        21.90        35.74        37.78        34.65        32.02 
TCGA-AX-A2H5 TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11V 
       71.24        20.52         0.39        27.85        75.72        19.56 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
      102.31        11.87        31.36        22.39        35.08        24.13 
TCGA-BS-A0U9 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16S 
       92.88        36.10        27.42        11.51        29.92        18.67 
TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR 
       28.08         0.72        18.25        18.84        17.29        71.61 
TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU 
       31.10        49.15        37.71        51.42        19.40        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A54A 
       16.34        54.15        11.08        29.10        27.35        14.70 
TCGA-FI-A2D2 TCGA-FI-A3PX TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       77.33        78.38        38.70        22.59         8.19         0.07 

$`AMP PEAK 35(16P11.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81        10.19       110.63        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
        1.38        27.09        61.87        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        14.40        18.87        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00        23.74         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        36.33        33.07        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O 
       34.95        25.51        11.21        18.41        20.25        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI 
       21.14        19.79        35.15        34.36        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        45.53        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        61.08        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       32.91        25.51        26.37        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 
       85.48        73.41        80.25        37.58         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82         0.20         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       73.28        16.73        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      225.50        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16N 
       15.72        37.32        36.36        37.51        36.79        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       22.92         1.41        13.22        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       15.88         4.27         2.20       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30        35.38         9.37        12.39       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        10.92        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        20.05        45.76        31.04        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       26.10        18.21        23.24        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                          0.07                           0.13 
  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                        118.19                         225.50 
  AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE 
                         28.59                          30.02 
[1] "0.1 - 118.2 (28.6)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.8"
D35V2, binary
                                cls
clus                               0   1
  AMP PEAK 35(16P11.2) MUTATED    34  29
  AMP PEAK 35(16P11.2) WILD-TYPE 256 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 35(16P11.2) MUTATED     34   29
  AMP PEAK 35(16P11.2) WILD-TYPE  256  195
     clus
vv    AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE
  NO                            34                            256
  YES                           29                            195
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 35(16P11.2) MUTATED                                        23
  AMP PEAK 35(16P11.2) WILD-TYPE                                     381
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 35(16P11.2) MUTATED                               2
  AMP PEAK 35(16P11.2) WILD-TYPE                            20
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 35(16P11.2) MUTATED                                  41
  AMP PEAK 35(16P11.2) WILD-TYPE                                72
D35V3, multiclass
                                         clus
vv                                        AMP PEAK 35(16P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           23
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 41
                                         clus
vv                                        AMP PEAK 35(16P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            381
  MIXED SEROUS AND ENDOMETRIOID                                       20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 35(16P11.2) MUTATED    41   3   3  10
  AMP PEAK 35(16P11.2) WILD-TYPE 330  19  13  30
D35V4, multiclass
    clus
vv   AMP PEAK 35(16P11.2) MUTATED AMP PEAK 35(16P11.2) WILD-TYPE
  R0                           41                            330
  R1                            3                             19
  R2                            3                             13
  RX                           10                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = AMP PEAK 36(17Q11.2) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 36(17Q11.2) MUTATED    48  23
  AMP PEAK 36(17Q11.2) WILD-TYPE 399  67
  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                            71                            466 
  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                            23                             67 
$`AMP PEAK 36(17Q11.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A1CP TCGA-B5-A0KB TCGA-BG-A0YV 
       41.06        10.19        57.80        36.39        27.09        12.56 
TCGA-E6-A8L9 TCGA-KJ-A3U4 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0R7 TCGA-A5-A1OG 
       33.30        36.00        39.52        37.02        17.59        31.99 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD 
       36.33       118.19        28.64        14.96        20.25        34.16 
TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0LI TCGA-AP-A5FX 
        1.64        16.87        63.91        36.89        97.71        36.13 
TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       13.28        34.65        25.51         4.77        30.12        71.24 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11I 
       17.75         2.96         0.30         0.39        27.29        75.72 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-BG-A0M4 TCGA-BG-A3PP 
       11.87        31.36        93.50        29.65        71.24        22.39 
TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A1NW TCGA-D1-A1O0 
       35.08        92.88        83.64        29.95         0.72         2.07 
TCGA-D1-A3DA TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A2CH 
       15.88        35.38        12.39       110.10        10.92        19.40 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS 
       26.96        16.34        23.90        32.71        19.27        22.03 
TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 
       12.59        20.05        29.10        32.52        11.38        77.33 
TCGA-FI-A2EX TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A915 TCGA-SL-A6J9 
        9.34        78.38        14.04         8.19         0.07 

$`AMP PEAK 36(17Q11.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       20.81       110.63        93.99        95.47        67.66        12.26 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 
       23.05        61.18        27.88         1.38        80.38        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        16.93         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 
       66.77        13.84        73.32        23.74         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       37.91        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       31.99        33.07        66.15        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        18.41        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        18.12        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N 
       21.99        23.31        86.07        48.03        45.53        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       43.82        40.11        77.39        32.91        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       37.58        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 
       43.82         0.20        20.52         0.30         0.26         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       72.62        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
       52.54       136.60        96.30        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.94        35.21        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98        35.90        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       89.59        63.58        86.99        66.48        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ 
       48.79         8.48        58.95         4.27        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        2.20        71.61       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        31.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       45.57        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        34.39        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       46.42        22.26        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.62        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       37.05        19.33        22.82        45.76        31.04        27.35 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14        14.70        16.96        68.38        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       25.22        96.69        59.01        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       41.56         1.74        17.75        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       18.21        23.24        21.30        38.70        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        20.75        18.28         0.23 

  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                          0.07                           0.13 
  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                        118.19                         225.50 
  AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE 
                         27.29                          30.15 
[1] "0.1 - 118.2 (27.3)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.6"
D36V2, binary
                                cls
clus                               0   1
  AMP PEAK 36(17Q11.2) MUTATED    37  30
  AMP PEAK 36(17Q11.2) WILD-TYPE 253 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(17Q11.2) MUTATED     37   30
  AMP PEAK 36(17Q11.2) WILD-TYPE  253  194
     clus
vv    AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE
  NO                            37                            253
  YES                           30                            194
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 36(17Q11.2) MUTATED                                        19
  AMP PEAK 36(17Q11.2) WILD-TYPE                                     385
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 36(17Q11.2) MUTATED                               6
  AMP PEAK 36(17Q11.2) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 36(17Q11.2) MUTATED                                  46
  AMP PEAK 36(17Q11.2) WILD-TYPE                                67
D36V3, multiclass
                                         clus
vv                                        AMP PEAK 36(17Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           19
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 46
                                         clus
vv                                        AMP PEAK 36(17Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            385
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 36(17Q11.2) MUTATED    39   7   6   7
  AMP PEAK 36(17Q11.2) WILD-TYPE 332  15  10  33
D36V4, multiclass
    clus
vv   AMP PEAK 36(17Q11.2) MUTATED AMP PEAK 36(17Q11.2) WILD-TYPE
  R0                           39                            332
  R1                            7                             15
  R2                            6                             10
  RX                            7                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = AMP PEAK 37(17Q12) MUTATION ANALYSIS
D37V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 37(17Q12) MUTATED    51  24
  AMP PEAK 37(17Q12) WILD-TYPE 396  66
  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                          75                          462 
  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                          24                           66 
$`AMP PEAK 37(17Q12) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2HF 
       41.06        10.19       110.63        36.39        23.05        27.88 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 TCGA-KJ-A3U4 
       80.38        22.06        16.93        33.30        10.19        36.00 
TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3QS 
       36.82        36.33        18.41        20.25        34.16        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0LH TCGA-AX-A0IU 
       16.87        20.78        63.91        45.53        36.36        35.74 
TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2HH 
       37.78        13.28        34.65        76.83         4.77        17.75 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 
        2.96        64.93        43.82         0.26         0.39        27.29 
TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       75.72        11.87        31.36        29.65        34.13        34.95 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BK-A26L TCGA-BS-A0U8 TCGA-D1-A0ZP TCGA-D1-A16G 
       20.94        71.24        24.13        97.41        29.95        27.42 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A2G0 TCGA-DI-A1NN TCGA-DI-A2QT 
       11.51        18.67        18.25        48.79        35.38        12.39 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR 
      110.10        79.10        26.96        54.15        19.27        17.62 
TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A 
       22.03        20.05        27.35        32.52        11.38        14.70 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI 
        9.34        28.93        30.67        59.28        78.38        17.75 
TCGA-KP-A3W4 TCGA-PG-A915 TCGA-SL-A6J9 
       18.21         8.19         0.07 

$`AMP PEAK 37(17Q12) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       20.81        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       61.18         1.38        27.09        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
        6.21        22.78        17.88        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ 
       19.89         5.88        66.77        13.84        73.32        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       25.51        14.96        11.21        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        86.07        48.03        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       57.47        27.39        30.02        60.66        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        77.39        32.91        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       25.91        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       38.24        30.74        31.13         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.30         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M7 
       41.06        18.61        20.19        19.33        35.21        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 
       13.78        14.73        14.01        15.45        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        86.99        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22         0.72        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        4.27        18.84        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30         9.37        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       18.84        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        45.76        31.04        29.10 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.14        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       25.22        96.69        59.01        41.56         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28         9.47        26.10        23.24        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                        0.07                         0.13 
  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                      110.63                       225.50 
  AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE 
                      27.420                       30.135 
[1] "0.1 - 110.6 (27.4)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.5"
D37V2, binary
                              cls
clus                             0   1
  AMP PEAK 37(17Q12) MUTATED    35  35
  AMP PEAK 37(17Q12) WILD-TYPE 255 189
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 37(17Q12) MUTATED     35   35
  AMP PEAK 37(17Q12) WILD-TYPE  255  189
     clus
vv    AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE
  NO                          35                          255
  YES                         35                          189
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 37(17Q12) MUTATED                                        20
  AMP PEAK 37(17Q12) WILD-TYPE                                     384
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 37(17Q12) MUTATED                               4
  AMP PEAK 37(17Q12) WILD-TYPE                            18
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 37(17Q12) MUTATED                                  51
  AMP PEAK 37(17Q12) WILD-TYPE                                62
D37V3, multiclass
                                         clus
vv                                        AMP PEAK 37(17Q12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         20
  MIXED SEROUS AND ENDOMETRIOID                                    4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               51
                                         clus
vv                                        AMP PEAK 37(17Q12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          384
  MIXED SEROUS AND ENDOMETRIOID                                     18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 37(17Q12) MUTATED    47   5   4   6
  AMP PEAK 37(17Q12) WILD-TYPE 324  17  12  34
D37V4, multiclass
    clus
vv   AMP PEAK 37(17Q12) MUTATED AMP PEAK 37(17Q12) WILD-TYPE
  R0                         47                          324
  R1                          5                           17
  R2                          4                           12
  RX                          6                           34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = AMP PEAK 38(17Q25.1) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 38(17Q25.1) MUTATED    73  32
  AMP PEAK 38(17Q25.1) WILD-TYPE 374  58
  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                           105                            432 
  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                            32                             58 
$`AMP PEAK 38(17Q25.1) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B 
       41.06        20.81        10.19       110.63        57.80        67.66 
TCGA-AX-A1CR TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       23.05        27.88        80.38        27.09        22.06        66.41 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GR 
       16.93        33.30        23.74        39.52        65.75        36.82 
TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       17.59        36.33        28.64        20.25        14.43        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A 
       18.12        22.26        16.87        20.78        21.99        63.91 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AP-A5FX 
       36.89        48.79       125.42        36.36        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CF TCGA-AX-A1CN 
        0.56        35.74        37.78        13.28        76.83        37.58 
TCGA-AX-A2H2 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
        4.77        17.75         2.96         0.56        43.82        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I 
        0.30         0.26         0.39        27.29        27.85        75.72 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A3PP 
      102.31        11.87        31.36        20.94        71.24        22.39 
TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ 
       35.08        16.64        61.87        92.88        29.95        22.55 
TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 
       39.48        11.51        18.67         0.72         2.07        48.79 
TCGA-D1-A2G7 TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO 
       58.95        17.29       109.08        25.91        35.38         9.37 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ 
      110.10        79.10        34.39        22.26        16.34        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ 
       32.71        19.27        22.03        12.59        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2F9 
       27.35        11.38        14.70        68.38        96.69        59.28 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W4 
       78.38         1.74        17.75        14.04         9.47        18.21 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-SL-A6J9 
       38.70         8.19         0.07 

$`AMP PEAK 38(17Q25.1) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A3G3 
       93.99        95.47        12.26        36.39        61.18         1.38 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
        4.44        47.84         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        37.91        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07       118.19        66.15        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96        11.21        18.41        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       35.15        34.36        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       48.03        45.53        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H4 TCGA-AX-A2H5 
       34.09        85.48        73.41        80.25        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       40.80        81.37        34.32        46.49        38.24        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G7 
       31.13        64.93         0.23         0.20         0.20         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       36.49        72.62        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      225.50        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       19.33        35.21        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98        35.90        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ 
       24.33        85.55        78.21         4.80        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       83.64        86.99        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        28.67        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN 
        3.95         8.48        15.88         4.27        18.84         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
       71.61       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        19.40        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX 
       35.15        38.07        27.16        46.42        26.96        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT 
       23.34        23.34        33.34        18.84        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       32.78        15.81        11.08        37.05        19.33        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 
       45.76        31.04        32.52        14.14        16.96        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       77.33         7.99        25.22        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB 
       30.67        41.56        13.28        26.10        23.24        21.30 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                          0.07                           0.13 
  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                        125.42                         225.50 
  AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE 
                        25.910                         30.705 
[1] "0.1 - 125.4 (25.9)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.5"
D38V2, binary
                                cls
clus                               0   1
  AMP PEAK 38(17Q25.1) MUTATED    51  46
  AMP PEAK 38(17Q25.1) WILD-TYPE 239 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(17Q25.1) MUTATED     51   46
  AMP PEAK 38(17Q25.1) WILD-TYPE  239  178
     clus
vv    AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE
  NO                            51                            239
  YES                           46                            178
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 38(17Q25.1) MUTATED                                        39
  AMP PEAK 38(17Q25.1) WILD-TYPE                                     365
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 38(17Q25.1) MUTATED                               9
  AMP PEAK 38(17Q25.1) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 38(17Q25.1) MUTATED                                  57
  AMP PEAK 38(17Q25.1) WILD-TYPE                                56
D38V3, multiclass
                                         clus
vv                                        AMP PEAK 38(17Q25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           39
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 57
                                         clus
vv                                        AMP PEAK 38(17Q25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            365
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 38(17Q25.1) MUTATED    66   4   5  13
  AMP PEAK 38(17Q25.1) WILD-TYPE 305  18  11  27
D38V4, multiclass
    clus
vv   AMP PEAK 38(17Q25.1) MUTATED AMP PEAK 38(17Q25.1) WILD-TYPE
  R0                           66                            305
  R1                            4                             18
  R2                            5                             11
  RX                           13                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = AMP PEAK 39(18P11.31) MUTATION ANALYSIS
D39V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 39(18P11.31) MUTATED    73  23
  AMP PEAK 39(18P11.31) WILD-TYPE 374  67
  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                             96                             441 
  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                             23                              67 
$`AMP PEAK 39(18P11.31) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A2H8 TCGA-AX-A3G3 
       41.06        20.81        10.19        93.99        61.18         1.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-D1-A3JP TCGA-E6-A8L9 
       27.09        22.06        66.41        51.55        16.93        33.30 
TCGA-EY-A212 TCGA-EY-A547 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-5B-A90C TCGA-A5-A0G5 
       10.19        17.92         5.88        36.00        39.52        37.02 
TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LP 
      105.37        36.82        37.91        31.99        36.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
       14.43        34.16        22.26        21.21        16.87        16.87 
TCGA-AJ-A6NU TCGA-AP-A05A TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO 
       20.78        63.91        48.79       125.42        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA 
       46.78        21.90        36.13        37.78        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HC 
       25.91        76.83         4.77        30.12        71.24        34.32 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3GI TCGA-B5-A0K8 
        2.96        64.93         0.56        43.82         0.39        27.85 
TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A2AE TCGA-BK-A0CC 
       75.72        29.65        34.13        34.95        23.70        35.08 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A1NW 
       24.13        92.88        39.48        37.32        18.67         0.72 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DI-A1NN 
       48.79        58.95        18.84        17.29        71.61        35.38 
TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ 
        9.37       110.10        79.10        51.42        19.40        27.16 
TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-FI-A2CY 
       22.26        17.62        12.59        20.05        29.10        68.38 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       59.01         9.34        28.93        30.67        59.28        78.38 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       14.04         9.47        23.24        38.70         8.19         4.44 

$`AMP PEAK 39(18P11.31) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        95.47        67.66        12.26        36.39 
TCGA-AX-A1CR TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 
       23.05        27.88        80.38        61.87        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
        1.81        19.79         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        14.40        18.87        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32        23.74         0.43        10.29       106.88       149.56 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       42.35        15.95        31.99        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        25.51        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       14.76        22.32        12.82         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        48.03        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.91        34.65        25.51        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HG 
       80.25        37.58        40.80        81.37        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       17.75        30.74        31.13         0.23         0.20         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       27.29        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       39.35        27.65        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.01        15.45        15.45         9.57        20.02        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       11.31        22.39        35.90        34.98        35.90        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       22.55         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU 
        8.48        15.88         4.27         2.20       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        12.39        31.10        23.38        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       46.42        26.96        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS 
       23.90        33.34        32.71        19.27        18.84        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        45.76        31.04        27.35        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.14        14.70        16.96        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 
       25.22        96.69        41.56         1.74        17.75        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       26.10        18.21        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                           0.39                            0.07 
  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                         125.42                          225.50 
  AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE 
                          31.33                           29.69 
[1] "0.4 - 125.4 (31.3)" "0.1 - 225.5 (29.7)"
[1] "hr=" "1.6"
D39V2, binary
                                 cls
clus                                0   1
  AMP PEAK 39(18P11.31) MUTATED    52  40
  AMP PEAK 39(18P11.31) WILD-TYPE 238 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 39(18P11.31) MUTATED     52   40
  AMP PEAK 39(18P11.31) WILD-TYPE  238  184
     clus
vv    AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE
  NO                             52                             238
  YES                            40                             184
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 39(18P11.31) MUTATED                                        30
  AMP PEAK 39(18P11.31) WILD-TYPE                                     374
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 39(18P11.31) MUTATED                               6
  AMP PEAK 39(18P11.31) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 39(18P11.31) MUTATED                                  60
  AMP PEAK 39(18P11.31) WILD-TYPE                                53
D39V3, multiclass
                                         clus
vv                                        AMP PEAK 39(18P11.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            30
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  60
                                         clus
vv                                        AMP PEAK 39(18P11.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             374
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 39(18P11.31) MUTATED    63   3   7   8
  AMP PEAK 39(18P11.31) WILD-TYPE 308  19   9  32
D39V4, multiclass
    clus
vv   AMP PEAK 39(18P11.31) MUTATED AMP PEAK 39(18P11.31) WILD-TYPE
  R0                            63                             308
  R1                             3                              19
  R2                             7                               9
  RX                             8                              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = AMP PEAK 40(18Q11.2) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 40(18Q11.2) MUTATED    50  19
  AMP PEAK 40(18Q11.2) WILD-TYPE 397  71
  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                            69                            468 
  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                            19                             71 
$`AMP PEAK 40(18Q11.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A2H8 
       41.06        29.39        20.81        10.19        93.99        61.18 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-E6-A8L9 TCGA-EY-A212 
        1.38        80.38        66.41        51.55        33.30        10.19 
TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0GE TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-AJ-A23N 
        5.88        39.52       105.37        37.91        36.33        14.43 
TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05J TCGA-AP-A0L8 
       22.26        21.21        16.87        16.87        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A2H4 
      125.42        33.40        46.78        21.90        36.13        30.12 
TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
       71.24        34.32        75.72        11.87        31.36        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       34.13        34.95        23.70        22.39        35.08        24.13 
TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A2G0 
       92.88        22.55        39.48        11.51        18.67        48.79 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
       58.95        18.84        71.61        35.38         9.37       110.10 
TCGA-E6-A1LZ TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2ON 
       79.10        34.39        26.96        17.62        12.59        20.05 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F9 
       29.10        27.35        11.38        59.01        28.93        59.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A915 
       26.10        18.21         8.19 

$`AMP PEAK 40(18Q11.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AP-A053 
       88.18        60.53        30.15        16.83        18.08       110.63 
TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR 
       57.80        95.47        67.66        12.26        36.39        23.05 
TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 
       27.88        27.09        22.06        61.87        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        16.93         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       22.78        17.88        14.40        18.87        17.92        19.89 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
       32.78       112.54       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95        31.99        31.99        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        20.25        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16        18.12        18.90        33.90         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        45.53        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       20.91       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       51.12         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       40.80        81.37        46.49        38.24        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       51.45        14.70        48.43        52.54       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       93.50        71.84        39.35        27.65        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 
       13.78        14.73        14.01        15.45        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.02        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       23.93         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN 
        3.95         8.48        15.88         4.27        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       32.71        19.27        18.84        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO 
       15.81        11.08        37.05        19.33        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        32.52        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX 
       39.88        77.33         7.99        25.22        96.69         9.34 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        41.56        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       13.28         9.47        23.24        21.30        38.70        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                          1.38                           0.07 
  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                        125.42                         225.50 
  AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE 
                        31.360                         29.785 
[1] "1.4 - 125.4 (31.4)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.8"
D40V2, binary
                                cls
clus                               0   1
  AMP PEAK 40(18Q11.2) MUTATED    32  35
  AMP PEAK 40(18Q11.2) WILD-TYPE 258 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(18Q11.2) MUTATED     32   35
  AMP PEAK 40(18Q11.2) WILD-TYPE  258  189
     clus
vv    AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE
  NO                            32                            258
  YES                           35                            189
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 40(18Q11.2) MUTATED                                        21
  AMP PEAK 40(18Q11.2) WILD-TYPE                                     383
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 40(18Q11.2) MUTATED                               4
  AMP PEAK 40(18Q11.2) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 40(18Q11.2) MUTATED                                  44
  AMP PEAK 40(18Q11.2) WILD-TYPE                                69
D40V3, multiclass
                                         clus
vv                                        AMP PEAK 40(18Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           21
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 40(18Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            383
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 40(18Q11.2) MUTATED    43   1   4   9
  AMP PEAK 40(18Q11.2) WILD-TYPE 328  21  12  31
D40V4, multiclass
    clus
vv   AMP PEAK 40(18Q11.2) MUTATED AMP PEAK 40(18Q11.2) WILD-TYPE
  R0                           43                            328
  R1                            1                             21
  R2                            4                             12
  RX                            9                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = AMP PEAK 41(19P13.2) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 41(19P13.2) MUTATED    68  23
  AMP PEAK 41(19P13.2) WILD-TYPE 379  67
  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                            91                            446 
  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                            23                             67 
$`AMP PEAK 41(19P13.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       41.06        29.39       110.63        93.99        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0VT TCGA-BG-A0YV 
       23.05        61.18        27.88        80.38        51.55        12.56 
TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A547 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A1OH 
       33.30        10.19        17.92        23.74        65.75        36.33 
TCGA-AJ-A23N TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A8CW 
       14.43        18.90         1.64        22.26        21.21         0.13 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       63.91        45.53        36.89        48.79       125.42        97.71 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A2H2 TCGA-AX-A2H5 
       46.78        36.13        37.78        34.65         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3GI 
       40.80        64.93        43.82        20.52         0.30         0.39 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A3S1 
       27.85        75.72       102.31        11.87        39.35        29.65 
TCGA-B5-A5OE TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I 
       34.95        35.08        92.88        83.64        22.55        11.51 
TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 
       18.67        13.22         0.72        18.25         2.07        58.95 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY 
       18.84        17.29       109.08        35.38        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       79.10        10.92        37.71        51.52        51.42        19.40 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A210 
       26.96        22.26        16.34        23.90        17.62        12.59 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       29.10        27.35        11.38        68.38        77.33        96.69 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A7D5 
       30.67        59.28         1.74        14.04        26.10        38.70 
TCGA-PG-A915 
        8.19 

$`AMP PEAK 41(19P13.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A3G3 TCGA-B5-A0KB 
       10.19        57.80        95.47        12.26         1.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       22.06        66.41        61.87        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        16.93         6.21        22.78        17.88 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       14.40        18.87        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       31.99        31.99        33.07       118.19        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       34.16        18.12        33.90        14.66        22.49        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.62        20.91       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        21.90         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        32.91        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       30.12        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74         2.96        31.13         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.30         0.26         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       225.50        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       51.45        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        93.50        71.84        27.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       22.92         1.41        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN 
        3.95        48.79         8.48        15.88         4.27         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
       71.61       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT 
       16.31        39.29        36.62        24.30         9.37        12.39 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        49.15        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       57.60        34.39        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       46.42        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       11.08        37.05        19.33        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 
       31.04        32.52        14.14        14.70        16.96        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV 
        7.99        25.22        59.01         9.34        28.93        41.56 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
       78.38        17.75        13.28         9.47        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                          0.13                           0.07 
  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                        125.42                         225.50 
  AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE 
                        31.100                         29.785 
[1] "0.1 - 125.4 (31.1)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.6"
D41V2, binary
                                cls
clus                               0   1
  AMP PEAK 41(19P13.2) MUTATED    43  42
  AMP PEAK 41(19P13.2) WILD-TYPE 247 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 41(19P13.2) MUTATED     43   42
  AMP PEAK 41(19P13.2) WILD-TYPE  247  182
     clus
vv    AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE
  NO                            43                            247
  YES                           42                            182
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 41(19P13.2) MUTATED                                        29
  AMP PEAK 41(19P13.2) WILD-TYPE                                     375
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 41(19P13.2) MUTATED                               8
  AMP PEAK 41(19P13.2) WILD-TYPE                            14
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 41(19P13.2) MUTATED                                  55
  AMP PEAK 41(19P13.2) WILD-TYPE                                58
D41V3, multiclass
                                         clus
vv                                        AMP PEAK 41(19P13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           29
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 55
                                         clus
vv                                        AMP PEAK 41(19P13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            375
  MIXED SEROUS AND ENDOMETRIOID                                       14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 41(19P13.2) MUTATED    60   5   4   9
  AMP PEAK 41(19P13.2) WILD-TYPE 311  17  12  31
D41V4, multiclass
    clus
vv   AMP PEAK 41(19P13.2) MUTATED AMP PEAK 41(19P13.2) WILD-TYPE
  R0                           60                            311
  R1                            5                             17
  R2                            4                             12
  RX                            9                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = AMP PEAK 42(19P13.12) MUTATION ANALYSIS
D42V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 42(19P13.12) MUTATED    74  24
  AMP PEAK 42(19P13.12) WILD-TYPE 373  66
  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                             98                             439 
  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                             24                              66 
$`AMP PEAK 42(19P13.12) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A1CP 
       41.06        29.39        10.19       110.63        93.99        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0VT 
       23.05        61.18        27.88        80.38        66.41        51.55 
TCGA-BG-A0YV TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A547 TCGA-KP-A3VZ TCGA-5B-A90C 
       12.56        33.30        10.19        17.92        23.74        39.52 
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BI 
       37.02        65.75        36.33        14.96        14.43        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW 
        1.64        22.26        21.21        16.87        16.87         0.13 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ 
       63.91        45.53        48.79       125.42        97.71        46.78 
TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H2 
       36.13        35.74        37.78        34.65        25.51         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2IO TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 
       71.24        40.80        64.93        20.52         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3S1 
        0.39        27.85        75.72       102.31        31.36        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0MT TCGA-BK-A0CC TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       34.13        34.95        21.17        35.08        83.64        22.55 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NW TCGA-D1-A1NX 
       11.51        18.67        28.08        11.15         0.72        18.25 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DI-A1NN 
        2.07        58.95        18.84        17.29       109.08        35.38 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CH 
       31.10       110.10        10.92        37.71        51.52        19.40 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A210 
       26.96        22.26        16.34        23.90        17.62        12.59 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2F9 
       20.05        29.10        27.35        11.38        68.38        59.28 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       78.38         1.74        14.04        23.24        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`AMP PEAK 42(19P13.12) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A3G3 TCGA-B5-A0KB 
       57.80        95.47        67.66        12.26         1.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       22.06        61.87        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 
       47.84        16.93         6.21        22.78        17.88        14.40 
TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       36.00         0.43        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        18.41        20.25        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        34.16        18.12        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       35.11       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO 
       60.23        45.86        27.85        51.12        21.90         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        32.91        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        85.48        73.41        80.25        37.58        30.12 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
        2.96        31.13         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        11.87        52.54       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       93.50        71.84        39.35        27.65        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.90        31.00        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
        4.87        28.67        23.93         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
        1.78        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
        8.48        15.88         4.27         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30         9.37        12.39        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        34.39        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       46.42        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       11.08        37.05        19.33        22.82        45.76        31.04 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 
       32.52        14.14        14.70        16.96        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       30.67        41.56        17.75        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       18.21        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                           0.13                            0.07 
  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                         125.42                          225.50 
  AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE 
                         27.865                          30.150 
[1] "0.1 - 125.4 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.7"
D42V2, binary
                                 cls
clus                                0   1
  AMP PEAK 42(19P13.12) MUTATED    46  45
  AMP PEAK 42(19P13.12) WILD-TYPE 244 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 42(19P13.12) MUTATED     46   45
  AMP PEAK 42(19P13.12) WILD-TYPE  244  179
     clus
vv    AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE
  NO                             46                             244
  YES                            45                             179
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 42(19P13.12) MUTATED                                        30
  AMP PEAK 42(19P13.12) WILD-TYPE                                     374
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 42(19P13.12) MUTATED                               7
  AMP PEAK 42(19P13.12) WILD-TYPE                            15
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 42(19P13.12) MUTATED                                  62
  AMP PEAK 42(19P13.12) WILD-TYPE                                51
D42V3, multiclass
                                         clus
vv                                        AMP PEAK 42(19P13.12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            30
  MIXED SEROUS AND ENDOMETRIOID                                       7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  62
                                         clus
vv                                        AMP PEAK 42(19P13.12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             374
  MIXED SEROUS AND ENDOMETRIOID                                        15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 42(19P13.12) MUTATED    63   6   5   8
  AMP PEAK 42(19P13.12) WILD-TYPE 308  16  11  32
D42V4, multiclass
    clus
vv   AMP PEAK 42(19P13.12) MUTATED AMP PEAK 42(19P13.12) WILD-TYPE
  R0                            63                             308
  R1                             6                              16
  R2                             5                              11
  RX                             8                              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = AMP PEAK 43(19Q12) MUTATION ANALYSIS
D43V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 43(19Q12) MUTATED    86  34
  AMP PEAK 43(19Q12) WILD-TYPE 361  56
  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                         120                          417 
  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                          34                           56 
$`AMP PEAK 43(19Q12) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A1CR TCGA-AX-A2H8 
       41.06        20.81        10.19        57.80        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0VT TCGA-D1-A3JP TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KJ-A3U4 
       51.55        16.93        17.92         5.88        66.77        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       23.74        39.52        37.02        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       66.15        14.96        18.41        20.25        14.43        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       18.12        18.90         1.64        16.87        16.87        20.78 
TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        0.13        21.99        63.91        45.53        48.79       125.42 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW 
       36.36        97.71        46.78        36.13        35.74        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       34.65        25.51        32.02         4.77        71.24        40.80 
TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K8 
        2.96        20.52         0.30         0.30         0.39        27.85 
TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       75.72        11.87        31.36        29.65        34.13        34.95 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 
       22.39        35.08        24.13        16.64        92.88        83.64 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NW 
       22.55        39.48        27.42        11.51        18.67         0.72 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 
       18.25         2.07        17.29        71.61       109.08        25.91 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
        9.37        12.39        31.10       110.10        79.10        10.92 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM 
       51.52        51.42        19.40        22.26        16.34        32.71 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A4KR 
       17.62        22.03        15.81        12.59        29.10        11.38 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       14.70        68.38        59.01         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       59.28        41.56        78.38        17.75        14.04         9.47 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       26.10        23.24        38.70         8.19         4.44         0.07 

$`AMP PEAK 43(19Q12) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        93.99        95.47        67.66        12.26        36.39 
TCGA-BG-A0MS TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       47.84        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       14.40        18.87        19.89        13.84        73.32         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A2K5 
       42.35        15.95        31.99        33.07        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       34.95        25.51        11.21        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       35.15        34.36        33.90        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       15.95        14.76        22.32        12.82         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N 
      129.80        23.31        86.07        48.03        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ 
       12.62        20.91       117.99       110.37        66.25        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        21.90         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        77.39        13.28        32.91        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       37.58        30.12        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.20         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       27.29        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       28.67        23.93         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J 
       36.10        37.32        36.36        37.51        36.79        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        13.22        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KU 
       58.95        15.88         4.27        18.84         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        35.38        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX 
       35.15        38.07        27.16        46.42        26.96        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        19.27        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       16.11        32.78        11.08        37.05        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       20.05        45.76        31.04        27.35        32.52        14.14 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        39.88        77.33         7.99        25.22        96.69 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
        1.74        13.28        18.21        21.30        22.59        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                        0.07                         0.20 
  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                      125.42                       225.50 
  AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE 
                      26.005                       30.740 
[1] "0.1 - 125.4 (26.0)" "0.2 - 225.5 (30.7)"
[1] "hr=" "2.4"
D43V2, binary
                              cls
clus                             0   1
  AMP PEAK 43(19Q12) MUTATED    55  55
  AMP PEAK 43(19Q12) WILD-TYPE 235 169
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 43(19Q12) MUTATED     55   55
  AMP PEAK 43(19Q12) WILD-TYPE  235  169
     clus
vv    AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE
  NO                          55                          235
  YES                         55                          169
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 43(19Q12) MUTATED                                        32
  AMP PEAK 43(19Q12) WILD-TYPE                                     372
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 43(19Q12) MUTATED                              11
  AMP PEAK 43(19Q12) WILD-TYPE                            11
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 43(19Q12) MUTATED                                  78
  AMP PEAK 43(19Q12) WILD-TYPE                                35
D43V3, multiclass
                                         clus
vv                                        AMP PEAK 43(19Q12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         32
  MIXED SEROUS AND ENDOMETRIOID                                   11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               78
                                         clus
vv                                        AMP PEAK 43(19Q12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          372
  MIXED SEROUS AND ENDOMETRIOID                                     11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 43(19Q12) MUTATED    76   5   6  14
  AMP PEAK 43(19Q12) WILD-TYPE 295  17  10  26
D43V4, multiclass
    clus
vv   AMP PEAK 43(19Q12) MUTATED AMP PEAK 43(19Q12) WILD-TYPE
  R0                         76                          295
  R1                          5                           17
  R2                          6                           10
  RX                         14                           26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = AMP PEAK 44(20P13) MUTATION ANALYSIS
D44V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 44(20P13) MUTATED    90  27
  AMP PEAK 44(20P13) WILD-TYPE 357  63
  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                         117                          420 
  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                          27                           63 
$`AMP PEAK 44(20P13) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CR TCGA-B5-A0JN 
       20.81        10.19        57.80        93.99        23.05        80.38 
TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A102 
       27.09        61.87        51.55        12.56         1.81         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A214 TCGA-FI-A2CX 
       47.84        33.30         6.21        10.19        14.40        66.77 
TCGA-KP-A3VZ TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       23.74        37.02        65.75        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QN 
       66.15        25.51        14.96        20.25        14.43        35.15 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AP-A0L9 TCGA-AP-A1DM 
       18.90         1.64        22.26        16.87       125.42        55.89 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA 
       31.30        46.78        35.74        37.78        34.65        32.02 
TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX 
       25.91         4.77        30.12         2.96        64.93        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A11I 
        0.20         0.26         0.30         0.39        55.30        75.72 
TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
       73.64        19.56        11.87        31.36       136.60        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BK-A0CC 
       27.65        29.65        34.13        52.83        15.45        35.08 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 
       31.00        24.13        16.64        13.18         4.80        92.88 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
       72.72        83.64        28.67        22.55        37.32        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A3DH TCGA-DF-A2L0 
       29.92        31.07        18.67         0.72        18.84        25.91 
TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
        9.37        79.10        10.92        37.71        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC 
       19.40        34.39        35.15        26.96        22.26        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OQ TCGA-EY-A3L3 
       23.90        32.71        17.62        22.03        29.10        27.35 
TCGA-EY-A54A TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       14.70        59.01         9.34        28.93        30.67        59.28 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 
       78.38        17.75        14.04         9.47        26.10        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       22.59         8.19         0.07 

$`AMP PEAK 44(20P13) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       18.08       110.63        95.47        67.66        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A220 
       61.18        27.88         1.38        22.06        66.41        14.27 
TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 
       19.79        16.93        22.78        17.88        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
       19.89         5.88        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN 
       32.78       112.54       105.37       123.68        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K4 TCGA-A5-A2K5 
       42.35        15.95        31.99        33.07        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       34.95        11.21        18.41        10.26        21.14        19.79 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        34.16        18.12        33.90        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91        48.79       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       90.97        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        61.08        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       32.91        25.51        26.37        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        38.24        17.75        30.74        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 
        0.23         0.20         0.56        20.52         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       18.35        14.47        56.91        86.37        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N 
       59.84       185.79       113.36        88.34        54.44        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA 
       50.89        51.45        14.70        48.43        52.54        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       93.50        71.84        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       11.31        22.39        35.90        34.98        35.90        31.76 
TCGA-BK-A13C TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       24.99        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41       114.90        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A101 
       29.95         8.55         0.56         4.87        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        27.42        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
        4.27        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30        35.38        12.39        31.10       110.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX 
       50.73        38.07        27.16        46.42        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        19.27        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       20.05        45.76        31.04        32.52        11.38        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC 
       96.69        41.56         1.74        13.28        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       21.30        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                        0.07                         0.13 
  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                       136.6                        225.5 
  AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE 
                       28.67                        30.15 
[1] "0.1 - 136.6 (28.7)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.7"
D44V2, binary
                              cls
clus                             0   1
  AMP PEAK 44(20P13) MUTATED    65  46
  AMP PEAK 44(20P13) WILD-TYPE 225 178
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(20P13) MUTATED     65   46
  AMP PEAK 44(20P13) WILD-TYPE  225  178
     clus
vv    AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE
  NO                          65                          225
  YES                         46                          178
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 44(20P13) MUTATED                                        53
  AMP PEAK 44(20P13) WILD-TYPE                                     351
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 44(20P13) MUTATED                               5
  AMP PEAK 44(20P13) WILD-TYPE                            17
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 44(20P13) MUTATED                                  59
  AMP PEAK 44(20P13) WILD-TYPE                                54
D44V3, multiclass
                                         clus
vv                                        AMP PEAK 44(20P13) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         53
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               59
                                         clus
vv                                        AMP PEAK 44(20P13) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          351
  MIXED SEROUS AND ENDOMETRIOID                                     17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 44(20P13) MUTATED    76   4   6   9
  AMP PEAK 44(20P13) WILD-TYPE 295  18  10  31
D44V4, multiclass
    clus
vv   AMP PEAK 44(20P13) MUTATED AMP PEAK 44(20P13) WILD-TYPE
  R0                         76                          295
  R1                          4                           18
  R2                          6                           10
  RX                          9                           31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = AMP PEAK 45(20Q11.21) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 45(20Q11.21) MUTATED   107  44
  AMP PEAK 45(20Q11.21) WILD-TYPE 340  46
  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                            151                             386 
  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                             44                              46 
$`AMP PEAK 45(20Q11.21) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR 
       20.81        10.19        57.80        93.99        67.66        23.05 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       27.88         1.38        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       61.87        51.55         1.81         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KP-A3VZ 
        6.21        14.40        17.92         5.88        66.77        23.74 
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 
       39.52       149.56        37.02        31.99        36.33        66.15 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       28.64        25.51        14.96        20.25        14.43        21.14 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
       35.15        34.16        18.90         1.64        22.26        17.06 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       16.87        16.87        63.91        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IU 
      125.42        97.71        31.30        46.78        21.90        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 
       37.78        34.65        32.02        25.91         4.77        30.12 
TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        2.96         0.23         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 
        0.30         0.26         0.30         0.39        55.30        27.29 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MY 
       27.85        75.72        73.64        19.56       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD 
       31.36       136.60        39.35        27.65        29.65        34.13 
TCGA-B5-A5OE TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       34.95        52.83        15.45        35.08        31.00        24.13 
TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZQ 
       13.18         4.80        92.88        72.72        83.64         8.55 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 
       37.32        11.51        29.92        31.07        18.67        14.73 
TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS 
       28.08         0.72         2.07        18.84        71.61       109.08 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       25.91        35.38        12.39       110.10        79.10        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV 
       49.15        37.71        51.52        51.42        19.40        35.15 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR 
       26.96        22.26        16.34        23.90        32.71        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ 
       22.03        11.08        37.05        12.59        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       27.35        32.52        14.70        77.33        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        30.67        41.56        78.38        17.75        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
        9.47        26.10        38.70        22.59         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK 45(20Q11.21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
       18.08       110.63        95.47        12.26        36.39        61.18 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK TCGA-EY-A1GQ 
       12.56        14.27        19.79        16.93        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       10.19        18.87        19.89        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        0.43        10.29       106.88        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 
       42.35        15.95        31.99        33.07       118.19        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QO 
       34.95        11.21        18.41        10.26        19.79        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE 
       18.12        33.90        14.66        22.49        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O 
       21.99        23.31        86.07        48.03        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        90.97        55.89        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       57.47        27.39        30.02        60.66        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        25.51        26.37 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3G8 
       17.75        30.74        31.13        64.93         0.20         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       18.35        14.47        56.91        86.37        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        88.34        54.44        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        77.23        73.28        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC 
       48.43        52.54        96.30        93.50        71.84        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        52.01        34.29        52.64        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 
       35.90        31.76        24.99        16.64        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI 
       46.95        24.33        85.55        78.21        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       82.39        81.57        73.25        59.51        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS 
       86.99        66.48        16.83        29.95         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       27.42        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV 
       15.88         4.27        17.29         2.20       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
        9.37        31.10        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.04         7.36        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ 
       46.26        57.60        34.39        50.73        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       46.42        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GO 
       24.36        27.16        23.34        23.34        33.34        19.27 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A2OM 
       18.84        16.11        32.78        15.81        19.33        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       45.76        31.04        11.38        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-H5-A2HR 
       39.88         7.99        25.22        96.69        59.28         1.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        18.21        23.24        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                           0.07                            0.13 
  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                         149.56                          225.50 
  AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE 
                          27.85                           30.74 
[1] "0.1 - 149.6 (27.9)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.8"
D45V2, binary
                                 cls
clus                                0   1
  AMP PEAK 45(20Q11.21) MUTATED    82  57
  AMP PEAK 45(20Q11.21) WILD-TYPE 208 167
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 45(20Q11.21) MUTATED     82   57
  AMP PEAK 45(20Q11.21) WILD-TYPE  208  167
     clus
vv    AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE
  NO                             82                             208
  YES                            57                             167
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 45(20Q11.21) MUTATED                                        65
  AMP PEAK 45(20Q11.21) WILD-TYPE                                     339
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 45(20Q11.21) MUTATED                               6
  AMP PEAK 45(20Q11.21) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 45(20Q11.21) MUTATED                                  81
  AMP PEAK 45(20Q11.21) WILD-TYPE                                32
D45V3, multiclass
                                         clus
vv                                        AMP PEAK 45(20Q11.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            65
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  81
                                         clus
vv                                        AMP PEAK 45(20Q11.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             339
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 45(20Q11.21) MUTATED    93   5   9  13
  AMP PEAK 45(20Q11.21) WILD-TYPE 278  17   7  27
D45V4, multiclass
    clus
vv   AMP PEAK 45(20Q11.21) MUTATED AMP PEAK 45(20Q11.21) WILD-TYPE
  R0                            93                             278
  R1                             5                              17
  R2                             9                               7
  RX                            13                              27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = AMP PEAK 46(20Q13.12) MUTATION ANALYSIS
D46V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 46(20Q13.12) MUTATED   111  40
  AMP PEAK 46(20Q13.12) WILD-TYPE 336  50
  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                            151                             386 
  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                             40                              50 
$`AMP PEAK 46(20Q13.12) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A06B 
       41.06        20.81        10.19       110.63        93.99        67.66 
TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS 
       23.05         1.38        80.38        27.09        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       51.55        12.56         1.81         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CX TCGA-KP-A3VZ 
        6.21        14.40        17.92         5.88        66.77        23.74 
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       39.52       149.56        37.91        31.99        36.33       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       66.15        28.64        25.51        20.25        14.43        21.14 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS 
       35.15        34.16        18.90         1.64        22.26        16.87 
TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ 
       16.87        63.91       125.42        97.71        31.30        46.78 
TCGA-AP-A3K1 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       21.90        35.74        37.78        34.65        25.51        32.02 
TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FS 
       25.91         4.77        30.12        71.24         2.96         0.23 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V 
        0.39        55.30        27.85        75.72        73.64        19.56 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FB 
      225.50       102.31        11.87        31.36       136.60        93.50 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BK-A0CC 
       39.35        29.65        34.95        52.83        15.45        35.08 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 
       24.13        13.18         4.80        92.88        72.72        83.64 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       29.95         8.55        37.32        11.51        29.92        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NW 
       18.67         3.95        30.15        14.73        28.08         0.72 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 
       18.25         2.07        18.84        71.61       109.08        25.91 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       35.38        12.39       110.10        79.10        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 
       37.71        51.52        51.42        19.40        35.15        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       22.26        16.34        23.90        32.71        17.62        22.03 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       11.08        37.05        12.59        20.05        29.10        27.35 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       11.38        14.70        68.38        77.33        59.01         9.34 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38        17.75        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
        9.47        26.10        38.70        22.59         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK 46(20Q13.12) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF 
       57.80        95.47        12.26        36.39        61.18        27.88 
TCGA-BG-A0M6 TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A3JP TCGA-EY-A1GK TCGA-EY-A1GQ 
       22.06        14.27        19.79        16.93        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       10.19        18.87        19.89        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 
       42.35        15.95        31.99        33.07        24.72        34.95 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QO 
       14.96        11.21        18.41        10.26        19.79        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       18.12        33.90        14.66        22.49        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        48.03        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        12.62        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        90.97        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       60.23        45.86        27.85        51.12        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.28        32.91        26.37        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       73.41        80.25        37.58        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         0.56         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       86.37        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       73.28        16.73        19.50        18.41        17.36        16.57 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA 
       50.89        51.45        14.70        48.43        52.54        96.30 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       71.84        27.65        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       34.29        52.64        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       11.31        22.39        35.90        34.98        35.90        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       31.76        24.99        16.64        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       81.57        73.25        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       66.48        16.83         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O 
       36.10        36.36        37.51        36.79        27.42        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        13.22        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU 
       58.95        15.88         4.27        17.29         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30         9.37        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       45.57        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY 
       66.90        46.26        57.60        34.39        50.73        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        46.42        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 
       19.27        18.84        16.11        32.78        15.81        19.33 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 
       22.82        45.76        31.04        32.52        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-H5-A2HR 
       39.88         7.99        25.22        96.69        28.93         1.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        18.21        23.24        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                           0.07                            0.13 
  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                         225.50                          185.79 
  AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE 
                          28.08                           30.59 
[1] "0.1 - 225.5 (28.1)" "0.1 - 185.8 (30.6)"
[1] "hr=" "2.1"
D46V2, binary
                                 cls
clus                                0   1
  AMP PEAK 46(20Q13.12) MUTATED    80  60
  AMP PEAK 46(20Q13.12) WILD-TYPE 210 164
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 46(20Q13.12) MUTATED     80   60
  AMP PEAK 46(20Q13.12) WILD-TYPE  210  164
     clus
vv    AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE
  NO                             80                             210
  YES                            60                             164
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 46(20Q13.12) MUTATED                                        67
  AMP PEAK 46(20Q13.12) WILD-TYPE                                     337
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 46(20Q13.12) MUTATED                               7
  AMP PEAK 46(20Q13.12) WILD-TYPE                            15
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 46(20Q13.12) MUTATED                                  78
  AMP PEAK 46(20Q13.12) WILD-TYPE                                35
D46V3, multiclass
                                         clus
vv                                        AMP PEAK 46(20Q13.12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            67
  MIXED SEROUS AND ENDOMETRIOID                                       7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  78
                                         clus
vv                                        AMP PEAK 46(20Q13.12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             337
  MIXED SEROUS AND ENDOMETRIOID                                        15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 46(20Q13.12) MUTATED    91   7   9  15
  AMP PEAK 46(20Q13.12) WILD-TYPE 280  15   7  25
D46V4, multiclass
    clus
vv   AMP PEAK 46(20Q13.12) MUTATED AMP PEAK 46(20Q13.12) WILD-TYPE
  R0                            91                             280
  R1                             7                              15
  R2                             9                               7
  RX                            15                              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = AMP PEAK 47(20Q13.33) MUTATION ANALYSIS
D47V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 47(20Q13.33) MUTATED   115  37
  AMP PEAK 47(20Q13.33) WILD-TYPE 332  53
  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                            152                             385 
  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                             37                              53 
$`AMP PEAK 47(20Q13.33) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       41.06        20.81        10.19        57.80        93.99        67.66 
TCGA-AX-A1CR TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 
       23.05        27.88         1.38        80.38        27.09        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A102 TCGA-D1-A2G5 
       61.87        51.55        12.56         1.81         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A72D 
       16.93        33.30         6.21        10.19        14.40         5.88 
TCGA-FI-A2CX TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GJ 
       66.77        23.74        39.52       149.56        37.02        65.75 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO 
       31.99        36.33       118.19        66.15        28.64        25.51 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD 
       14.96        20.25        14.43        21.14        35.15        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3QS TCGA-AJ-A3TW 
       18.12        18.90         1.64        22.26        16.87        16.87 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ 
       63.91        45.53       125.42        97.71        31.30        46.78 
TCGA-AP-A3K1 TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       21.90        35.74        37.78        34.65        25.51        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HK 
       25.91        76.83         4.77        30.12        71.24         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.23        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11I 
        0.30         0.39        55.30        58.75        27.85        75.72 
TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3F9 
       73.64        19.56       225.50       102.31        11.87       136.60 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0W1 TCGA-BG-A18C 
       39.35        27.65        29.65        34.95        52.83        15.45 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 
       35.08        24.13        13.18         4.80        61.87        92.88 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
       72.72        83.64         8.55        22.55        37.32        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW 
       29.92        31.07        18.67         3.95        28.08         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
        2.07        18.84        71.61       109.08        25.91        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        9.37        12.39       110.10        79.10        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B0 
       37.71        51.52        51.42        19.40        35.15        46.42 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
       22.26        54.15        32.71        17.62        22.03        11.08 
TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       37.05        12.59        20.05        29.10        27.35        11.38 
TCGA-EY-A54A TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       14.70        59.01         9.34        59.28        41.56        78.38 
TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       17.75         9.47        26.10        38.70        22.59         8.19 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`AMP PEAK 47(20Q13.33) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-BG-A0M6 
      110.63        95.47        12.26        36.39        61.18        22.06 
TCGA-BG-A220 TCGA-D1-A0ZO TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 
       14.27        19.79        22.78        17.88        18.87        17.92 
TCGA-EY-A549 TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 
       19.89        13.84        73.32        36.00         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      106.88        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      123.68        74.10        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O 
       33.07        24.72        34.95        11.21        18.41        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       19.79        34.36        33.90        14.66        22.49        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       14.76        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        12.62        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        90.97        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       60.23        45.86        27.85        51.12        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.28        32.91        26.37        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       80.25        37.58        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT 
       38.24        17.75        30.74        31.13        64.93         0.20 
TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.56         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       59.24        86.01        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N 
       59.84       185.79       113.36        88.34        54.44        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54        31.36        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       71.84        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.64        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       22.39        35.90        34.98        35.90        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.99        16.64        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41       114.90        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
       29.95         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        27.42        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN 
        8.48        58.95        15.88         4.27        17.29         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       45.57        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY 
       66.90        46.26        57.60        34.39        50.73        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        26.96        16.34        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        19.27        18.84        16.11        32.78        15.81 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 
       19.33        22.82        45.76        31.04        32.52        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 
       96.69        28.93        30.67         1.74        14.04        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                           0.07                            0.13 
  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                         225.50                          185.79 
  AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE 
                          27.98                           30.15 
[1] "0.1 - 225.5 (28.0)" "0.1 - 185.8 (30.1)"
[1] "hr=" "1.8"
D47V2, binary
                                 cls
clus                                0   1
  AMP PEAK 47(20Q13.33) MUTATED    85  56
  AMP PEAK 47(20Q13.33) WILD-TYPE 205 168
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 47(20Q13.33) MUTATED     85   56
  AMP PEAK 47(20Q13.33) WILD-TYPE  205  168
     clus
vv    AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE
  NO                             85                             205
  YES                            56                             168
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 47(20Q13.33) MUTATED                                        70
  AMP PEAK 47(20Q13.33) WILD-TYPE                                     334
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 47(20Q13.33) MUTATED                               6
  AMP PEAK 47(20Q13.33) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 47(20Q13.33) MUTATED                                  77
  AMP PEAK 47(20Q13.33) WILD-TYPE                                36
D47V3, multiclass
                                         clus
vv                                        AMP PEAK 47(20Q13.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            70
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  77
                                         clus
vv                                        AMP PEAK 47(20Q13.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             334
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 47(20Q13.33) MUTATED    91   7  10  16
  AMP PEAK 47(20Q13.33) WILD-TYPE 280  15   6  24
D47V4, multiclass
    clus
vv   AMP PEAK 47(20Q13.33) MUTATED AMP PEAK 47(20Q13.33) WILD-TYPE
  R0                            91                             280
  R1                             7                              15
  R2                            10                               6
  RX                            16                              24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = AMP PEAK 48(22Q12.2) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 48(22Q12.2) MUTATED    41  20
  AMP PEAK 48(22Q12.2) WILD-TYPE 406  70
  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                            61                            476 
  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                            20                             70 
$`AMP PEAK 48(22Q12.2) MUTATED`
TCGA-AJ-A2QM TCGA-AP-A0LF TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 TCGA-FI-A2CX 
       29.39        93.99        16.93        33.30        10.19        66.77 
TCGA-A5-A0G5 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AP-A05A TCGA-AP-A0L9 
       37.02        28.64        20.25        34.16        63.91       125.42 
TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 
       97.71        21.90        25.51        76.83         4.77        71.24 
TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A3S1 
        0.39        27.85       225.50       102.31        50.89        29.65 
TCGA-B5-A5OD TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0TE TCGA-D1-A0ZP 
       34.13        22.39        35.08        24.13         4.80        29.95 
TCGA-D1-A16R TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-DI-A1NN TCGA-EO-A1Y5 
        0.69        14.73        13.22         0.72        35.38        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GS 
       37.71        19.40        34.39        23.90        19.27        22.03 
TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY 
       20.05        27.35        32.52        11.38        14.70        68.38 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       96.69        59.01         9.34        28.93        30.67        41.56 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       14.04         9.47        18.21        38.70        22.59         8.19 
TCGA-QS-A8F1 
        4.44 

$`AMP PEAK 48(22Q12.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
        6.21        22.78        17.88        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       19.89         5.88        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
        0.43        39.52        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33        33.07       118.19        66.15        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O 
       25.51        14.96        11.21        18.41        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI 
       21.14        19.79        35.15        34.36        18.12        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        45.53        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA 
       77.39        13.28        32.91        34.65        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       25.91        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       30.12        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.20         0.56        43.82         0.20        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.26         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MW 
       19.50        18.41        17.36        16.57        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       93.50        71.84        39.35        27.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98        35.90        31.00        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       86.99        66.48        16.83         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        4.27        18.84        17.29         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        51.42        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        38.07        27.16        46.42        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        27.16        23.34        23.34        33.34        32.71 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.62        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       37.05        19.33        12.59        22.82        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       29.10        14.14        16.96        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 
       25.22        59.28        78.38         1.74        17.75        13.28 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       26.10        23.24        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                          0.39                           0.07 
  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                        225.50                         185.79 
  AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE 
                         27.85                          30.15 
[1] "0.4 - 225.5 (27.9)" "0.1 - 185.8 (30.1)"
[1] "hr=" "2.4"
D48V2, binary
                                cls
clus                               0   1
  AMP PEAK 48(22Q12.2) MUTATED    33  26
  AMP PEAK 48(22Q12.2) WILD-TYPE 257 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 48(22Q12.2) MUTATED     33   26
  AMP PEAK 48(22Q12.2) WILD-TYPE  257  198
     clus
vv    AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE
  NO                            33                            257
  YES                           26                            198
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 48(22Q12.2) MUTATED                                        11
  AMP PEAK 48(22Q12.2) WILD-TYPE                                     393
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 48(22Q12.2) MUTATED                               2
  AMP PEAK 48(22Q12.2) WILD-TYPE                            20
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 48(22Q12.2) MUTATED                                  49
  AMP PEAK 48(22Q12.2) WILD-TYPE                                64
D48V3, multiclass
                                         clus
vv                                        AMP PEAK 48(22Q12.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           11
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 49
                                         clus
vv                                        AMP PEAK 48(22Q12.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            393
  MIXED SEROUS AND ENDOMETRIOID                                       20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 48(22Q12.2) MUTATED    35   3   7   6
  AMP PEAK 48(22Q12.2) WILD-TYPE 336  19   9  34
D48V4, multiclass
    clus
vv   AMP PEAK 48(22Q12.2) MUTATED AMP PEAK 48(22Q12.2) WILD-TYPE
  R0                           35                            336
  R1                            3                             19
  R2                            7                              9
  RX                            6                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = AMP PEAK 49(XP11.23) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 49(XP11.23) MUTATED    71  19
  AMP PEAK 49(XP11.23) WILD-TYPE 376  71
  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                            90                            447 
  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                            19                             71 
$`AMP PEAK 49(XP11.23) MUTATED`
TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CR TCGA-BG-A0MS TCGA-BG-A0YV 
       20.81        57.80        93.99        23.05        61.87        12.56 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-KP-A3VZ 
        4.44        47.84         6.21        17.88        10.19        23.74 
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GV TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3EM 
       39.52        65.75        54.02       118.19        34.16        22.26 
TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A0LO TCGA-AP-A1DO 
       15.62        16.87        16.87         0.13        33.40        31.30 
TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A2H4 
       46.78        51.12        80.55        37.78        25.91        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT 
       40.80        81.37        17.75         0.39        56.91        55.30 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A5OD 
       27.29        57.76        77.23        73.28        50.89        34.13 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 
       19.33        20.94        35.21        71.24        15.42        52.83 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        35.08        31.00        24.13         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A165 TCGA-D1-A168 
       72.72        83.64        29.95        22.55         0.66        36.10 
TCGA-D1-A17R TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DI-A2QY TCGA-E6-A1M0 
       11.15         8.48        18.84        71.61       110.10        58.95 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       10.92        51.52        34.39        26.96        22.26        16.34 
TCGA-EY-A1GH TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OQ 
       23.34        17.62        22.03        37.05        19.33        29.10 
TCGA-EY-A3L3 TCGA-FI-A2CY TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PV 
       27.35        68.38         7.99        59.01         9.34        41.56 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       14.04         9.47        26.10        14.83         4.44         0.07 

$`AMP PEAK 49(XP11.23) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       18.08        10.19       110.63        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       36.39        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       22.06        66.41        51.55        14.27         1.81        19.79 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GK TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 
       16.93        33.30        22.78        14.40        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
        0.43        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW 
       60.53        46.55        73.87        36.82        28.27        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ 
       42.35        15.95        31.99        31.99        36.33        33.07 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       21.21        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       20.78         2.70        35.11       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       82.52        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       90.97        55.89        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       33.21        29.69        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE 
       32.91        34.65        25.51        26.37        32.02        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       76.83        85.48        73.41        80.25        37.58         4.77 
TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       71.24        34.32        46.49        38.24        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       18.35        14.47        86.37        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 
       69.27        71.44        48.59        36.49        72.62        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       52.04        32.09        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.95        18.61        20.19        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       22.39        34.98        35.90        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       92.88       114.90        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       29.33        32.58        15.72        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS 
       58.95        15.88         4.27        17.29         2.20       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        79.10         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       66.90        46.26        57.60        51.42        19.40        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        38.07        27.16        46.42        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT 
       23.90        33.34        32.71        19.27        18.84        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       32.78        15.81        11.08        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       45.76        31.04        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY 
       16.96        39.88        77.33        25.22        96.69        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 
       30.67        59.28        78.38         1.74        17.75        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        21.30        38.70        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                          0.07                           0.20 
  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                        118.19                         225.50 
  AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE 
                        29.525                         29.920 
[1] "0.1 - 118.2 (29.5)" "0.2 - 225.5 (29.9)"
[1] "hr=" "1.4"
D49V2, binary
                                cls
clus                               0   1
  AMP PEAK 49(XP11.23) MUTATED    47  37
  AMP PEAK 49(XP11.23) WILD-TYPE 243 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(XP11.23) MUTATED     47   37
  AMP PEAK 49(XP11.23) WILD-TYPE  243  187
     clus
vv    AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE
  NO                            47                            243
  YES                           37                            187
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 49(XP11.23) MUTATED                                        53
  AMP PEAK 49(XP11.23) WILD-TYPE                                     351
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 49(XP11.23) MUTATED                               4
  AMP PEAK 49(XP11.23) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 49(XP11.23) MUTATED                                  33
  AMP PEAK 49(XP11.23) WILD-TYPE                                80
D49V3, multiclass
                                         clus
vv                                        AMP PEAK 49(XP11.23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           53
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 33
                                         clus
vv                                        AMP PEAK 49(XP11.23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            351
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 49(XP11.23) MUTATED    61   3   5   8
  AMP PEAK 49(XP11.23) WILD-TYPE 310  19  11  32
D49V4, multiclass
    clus
vv   AMP PEAK 49(XP11.23) MUTATED AMP PEAK 49(XP11.23) WILD-TYPE
  R0                           61                            310
  R1                            3                             19
  R2                            5                             11
  RX                            8                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = AMP PEAK 50(XQ28) MUTATION ANALYSIS
D50V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 50(XQ28) MUTATED    68  24
  AMP PEAK 50(XQ28) WILD-TYPE 379  66
  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                         92                         445 
  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                         24                          66 
$`AMP PEAK 50(XQ28) MUTATED`
TCGA-AP-A053 TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0YV 
      110.63         1.38        80.38        22.06        61.87        12.56 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GQ 
        4.44        47.84        16.93        33.30         6.21        17.88 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       14.40        17.92         5.88        36.00        23.74        39.52 
TCGA-A5-A0GV TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A3BF TCGA-AJ-A3NG 
       54.02        14.96        18.41        14.43        18.12        15.62 
TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LO 
        0.13        63.91        45.53        36.89        48.79        33.40 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A2H2 
       31.30        46.78        51.12        36.13        80.55         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A3G4 TCGA-B5-A0JR 
       30.12        40.80        81.37        17.75         0.30        56.91 
TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MY TCGA-B5-A3S1 
       55.30        27.29        77.23        73.28        11.87        29.65 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 
       19.33        20.94        35.21        71.24        15.42        52.83 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        35.08        24.13        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A16R TCGA-D1-A17R 
       72.72        83.64         0.66        36.10         0.69        11.15 
TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A2QT 
        8.48        18.84        17.29       109.08        25.91        12.39 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CH 
      110.10        79.10        58.95        37.71        51.52        19.40 
TCGA-EO-A3AV TCGA-EO-A3KU TCGA-EY-A1GH TCGA-EY-A1GR TCGA-EY-A1GX TCGA-EY-A1H0 
       35.15        22.26        23.34        17.62        37.05        19.33 
TCGA-EY-A3L3 TCGA-FI-A2CY TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KP-A3W1 
       27.35        68.38         7.99        59.28        78.38         9.47 
TCGA-QS-A744 TCGA-QS-A8F1 
       14.83         4.44 

$`AMP PEAK 50(XQ28) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        20.81        10.19        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       27.09        66.41        51.55        14.27         1.81        19.79 
TCGA-EY-A1GK TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       22.78        10.19        18.87        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       73.32         0.43        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        65.75        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
       34.95        25.51        11.21        20.25        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        21.21        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
      129.80        21.99        23.31        86.07        48.03        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       55.89        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        21.90         0.56        13.58        33.21        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 
       76.83        85.48        73.41        80.25        37.58        71.24 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       34.32        46.49        38.24        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
        0.39        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       52.04        32.09        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       93.50        71.84        39.35        27.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.95        18.61        20.19        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        51.06        52.01        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       22.39        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       78.21        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       92.88       114.90        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A169 
        1.91         3.68        29.33        32.58        15.72        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.08        26.37        10.22         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR 
       48.79        58.95        15.88         4.27         2.20        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30        35.38         9.37        31.10        23.38 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.42        34.39        50.73        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       32.71        19.27        18.84        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       15.81        11.08        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        29.10        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       16.96        39.88        77.33        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI 
        9.34        28.93        30.67        41.56         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       14.04        13.28        26.10        18.21        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       39.95        24.95        23.64        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                       0.13                        0.07 
  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                     110.63                      225.50 
  AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE 
                      28.50                       29.95 
[1] "0.1 - 110.6 (28.5)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.9"
D50V2, binary
                             cls
clus                            0   1
  AMP PEAK 50(XQ28) MUTATED    45  41
  AMP PEAK 50(XQ28) WILD-TYPE 245 183
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 50(XQ28) MUTATED     45   41
  AMP PEAK 50(XQ28) WILD-TYPE  245  183
     clus
vv    AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE
  NO                         45                         245
  YES                        41                         183
[1] 2 2
[1] FALSE
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 50(XQ28) MUTATED                                        55
  AMP PEAK 50(XQ28) WILD-TYPE                                     349
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 50(XQ28) MUTATED                               4
  AMP PEAK 50(XQ28) WILD-TYPE                            18
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 50(XQ28) MUTATED                                  34
  AMP PEAK 50(XQ28) WILD-TYPE                                79
D50V3, multiclass
                                         clus
vv                                        AMP PEAK 50(XQ28) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        55
  MIXED SEROUS AND ENDOMETRIOID                                   4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              34
                                         clus
vv                                        AMP PEAK 50(XQ28) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         349
  MIXED SEROUS AND ENDOMETRIOID                                    18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 50(XQ28) MUTATED    65   2   6   8
  AMP PEAK 50(XQ28) WILD-TYPE 306  20  10  32
D50V4, multiclass
    clus
vv   AMP PEAK 50(XQ28) MUTATED AMP PEAK 50(XQ28) WILD-TYPE
  R0                        65                         306
  R1                         2                          20
  R2                         6                          10
  RX                         8                          32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK  1(1P36.21) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.21) MUTATED    51  20
  DEL PEAK  1(1P36.21) WILD-TYPE 396  70
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            71                            466 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            20                             70 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-B5-A0JN 
       10.19        57.80        67.66        36.39        23.05        80.38 
TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-EY-A214 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-A5-A0G2 
       66.41        16.93        14.40         5.88        23.74       149.56 
TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A23O 
       37.02        60.53        36.33        66.15        20.25        10.26 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05J 
       21.14        34.16        16.87        20.78        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AW-A1PO TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF 
       48.79       125.42         0.56        25.51        32.02        76.83 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3FX TCGA-B5-A11I TCGA-B5-A11P 
       37.58         4.77         2.96        43.82        75.72        52.04 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A16I 
       11.87        31.36        34.13        83.64         8.55        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1O0 TCGA-D1-A2G7 
       29.92        31.07        18.67        14.73         2.07        58.95 
TCGA-D1-A3DG TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y8 
        4.27        71.61        25.91        12.39       110.10        37.71 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       34.39        27.16        16.34        32.71        19.27        18.84 
TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A4KR TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       12.59        45.76        11.38        30.67        59.28        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 
        1.74        17.75        26.10        18.21        38.70 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D 
       18.08        20.81       110.63        93.99        95.47        12.26 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS 
       61.18        27.88         1.38        27.09        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       47.84        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        17.92        19.89        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 
       36.00         0.43        39.52        10.29       106.88        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
      118.19        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       11.21        18.41        14.43        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07        48.03        63.91        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        51.12        21.90        36.13        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        32.91        34.65        26.37        25.91        34.09 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       85.48        73.41        80.25        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       52.54       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        29.65        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        35.08        31.00        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR 
       63.58        86.99        66.48        16.83        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        27.42        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ 
        3.95        48.79         8.48        15.88        18.84        17.29 
TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20       109.08       100.83        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       19.40        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.62        22.03        16.11        32.78        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       37.05        19.33        22.82        20.05        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       27.35        32.52        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
        9.34        28.93        41.56        14.04        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        21.30        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          0.56                           0.07 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        149.56                         225.50 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        30.670                         29.785 
[1] "0.6 - 149.6 (30.7)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.9"
D51V2, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    37  31
  DEL PEAK  1(1P36.21) WILD-TYPE 253 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     37   31
  DEL PEAK  1(1P36.21) WILD-TYPE  253  193
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            37                            253
  YES                           31                            193
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                        28
  DEL PEAK  1(1P36.21) WILD-TYPE                                     376
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  1(1P36.21) MUTATED                               5
  DEL PEAK  1(1P36.21) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                  38
  DEL PEAK  1(1P36.21) WILD-TYPE                                75
D51V3, multiclass
                                         clus
vv                                        DEL PEAK  1(1P36.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           28
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        DEL PEAK  1(1P36.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            376
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.21) MUTATED    50   5   2   5
  DEL PEAK  1(1P36.21) WILD-TYPE 321  17  14  35
D51V4, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  R0                           50                            321
  R1                            5                             17
  R2                            2                             14
  RX                            5                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK  2(1P36.11) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1P36.11) MUTATED    57  25
  DEL PEAK  2(1P36.11) WILD-TYPE 390  65
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            82                            455 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            25                             65 
$`DEL PEAK  2(1P36.11) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR 
       20.81        10.19        57.80        67.66        36.39        23.05 
TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-EY-A212 TCGA-EY-A214 TCGA-KP-A3VZ 
        1.38        66.41        12.56        10.19        14.40        23.74 
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M 
      149.56        60.53        36.33        66.15        14.96        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H 
       10.26        21.14        34.16        16.87        16.87        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AW-A1PO TCGA-AX-A1C7 TCGA-AX-A1C8 
       36.89        48.79        97.71         0.56        34.65        25.51 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HG TCGA-AX-A3FX 
       32.02        76.83        30.12        71.24        38.24        43.82 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD 
       75.72        52.04        11.87        31.36        29.65        34.13 
TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 
       83.64         8.55        31.07        18.67         3.95        14.73 
TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KR 
       13.22         2.07        58.95         4.27        17.29        71.61 
TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EO-A1Y8 TCGA-EO-A3AS 
      109.08        25.91         9.37        12.39        37.71        34.39 
TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A210 
       27.16        16.34        32.71        19.27        18.84        12.59 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       20.05        45.76        29.10        27.35        32.52        11.38 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        30.67        41.56        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 
       14.04        26.10        18.21        38.70 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A2H8 
       18.08       110.63        93.99        95.47        12.26        61.18 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT 
       27.88        80.38        27.09        22.06        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       14.27         1.81        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 
       33.30         6.21        22.78        17.88        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
        0.43        39.52        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ 
      118.19        28.64        24.72        34.95        25.51        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       18.41        14.43        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       48.03        63.91        23.87        12.62        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        21.90        36.13        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.91        26.37        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58         4.77        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.23         0.20         0.56         0.20        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        51.45        14.70        48.43        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        93.50        71.84        39.35        27.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       22.39        35.90        34.98        35.90        35.08        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.76        24.99        24.13        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83        29.95         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       11.51        29.92        33.63        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       15.88        18.84         2.20       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        19.40        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        22.26        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A548 
       11.08        37.05        19.33        22.82        31.04        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-KP-A3W0 
       25.22        96.69        59.01         9.34        59.28        13.28 
TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
        9.47        23.24        21.30        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                          0.56                           0.07 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                        149.56                         225.50 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                         28.14                          30.08 
[1] "0.6 - 149.6 (28.1)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.4"
D52V2, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    42  35
  DEL PEAK  2(1P36.11) WILD-TYPE 248 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     42   35
  DEL PEAK  2(1P36.11) WILD-TYPE  248  189
     clus
vv    DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  NO                            42                            248
  YES                           35                            189
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                                        28
  DEL PEAK  2(1P36.11) WILD-TYPE                                     376
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  2(1P36.11) MUTATED                               5
  DEL PEAK  2(1P36.11) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                                  50
  DEL PEAK  2(1P36.11) WILD-TYPE                                63
D52V3, multiclass
                                         clus
vv                                        DEL PEAK  2(1P36.11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           28
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 50
                                         clus
vv                                        DEL PEAK  2(1P36.11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            376
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  2(1P36.11) MUTATED    53   7   5   6
  DEL PEAK  2(1P36.11) WILD-TYPE 318  15  11  34
D52V4, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                           53                            318
  R1                            7                             15
  R2                            5                             11
  RX                            6                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    17   8
  DEL PEAK  3(2P25.3) WILD-TYPE 430  82
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           25                           512 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                            8                            82 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-AJ-A3IA TCGA-AX-A3G3 TCGA-A5-A0GR TCGA-A5-A1OG TCGA-AJ-A3BI TCGA-AJ-A3EM 
       20.81         1.38        36.82        31.99        18.90        22.26 
TCGA-AP-A0L9 TCGA-AW-A1PO TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2HK TCGA-AX-A3FX 
      125.42         0.56        25.91        76.83         2.96        43.82 
TCGA-B5-A3FD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16R TCGA-D1-A1NW 
       39.35        92.88        22.55        11.51         0.69         0.72 
TCGA-DI-A1NO TCGA-EO-A1Y5 TCGA-EY-A2ON TCGA-FI-A2EY TCGA-H5-A2HR TCGA-PG-A5BC 
        9.37        10.92        20.05        28.93         1.74        23.24 
TCGA-PG-A914 
       22.59 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       18.08        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       80.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        36.33        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.12        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       45.86        27.85        51.12        21.90        36.13        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       32.02        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.23         0.20         0.56         0.20        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       71.84        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       17.29         2.20        71.61       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30        35.38        12.39        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       12.59        22.82        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
        9.34        30.67        59.28        41.56        78.38        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       14.04        13.28         9.47        26.10        18.21        21.30 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       125.42                        225.50 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                        22.26                         30.15 
[1] "0.6 - 125.4 (22.3)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.7"
D53V2, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED    17   6
  DEL PEAK  3(2P25.3) WILD-TYPE 273 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     17    6
  DEL PEAK  3(2P25.3) WILD-TYPE  273  218
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                           17                           273
  YES                           6                           218
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                        13
  DEL PEAK  3(2P25.3) WILD-TYPE                                     391
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  3(2P25.3) MUTATED                               2
  DEL PEAK  3(2P25.3) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                  11
  DEL PEAK  3(2P25.3) WILD-TYPE                               102
D53V3, multiclass
                                         clus
vv                                        DEL PEAK  3(2P25.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          13
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                11
                                         clus
vv                                        DEL PEAK  3(2P25.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           391
  MIXED SEROUS AND ENDOMETRIOID                                      20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2P25.3) MUTATED    17   0   2   2
  DEL PEAK  3(2P25.3) WILD-TYPE 354  22  14  38
D53V4, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          17                           354
  R1                           0                            22
  R2                           2                            14
  RX                           2                            38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    28  21
  DEL PEAK  4(2Q22.1) WILD-TYPE 419  69
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           49                           488 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           21                            69 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-AX-A1CR TCGA-B5-A0JN TCGA-EY-A212 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-AJ-A23M 
       23.05        80.38        10.19        23.74        39.52        20.25 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05H 
       34.16        18.12        16.87        16.87        21.99        45.53 
TCGA-AP-A0L9 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A2H2 TCGA-AX-A2H4 
      125.42        36.13         0.56        37.78         4.77        30.12 
TCGA-AX-A3G1 TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C 
       20.52       102.31        11.87        29.65        34.13        15.45 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-D1-A16I 
       22.39        35.08        31.00         4.80        92.88        11.51 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NO 
        2.07         4.27        18.84       109.08        25.91         9.37 
TCGA-EO-A1Y7 TCGA-EO-A2CH TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A2ON 
       49.15        19.40        54.15        17.62        11.08        20.05 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A5BC 
       29.10        32.52        11.38        41.56         1.74        23.24 
TCGA-PG-A915 
        8.19 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF 
       95.47        67.66        12.26        36.39        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 
       16.93        33.30         6.21        22.78        17.88        14.40 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32        36.00         0.43        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       28.64        24.72        34.95        25.51        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       18.41        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12        21.90        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       32.91        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.20         0.56        43.82         0.20         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        51.45        14.70        48.43        52.54        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98        35.90        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
        8.48        58.95        15.88        17.29         2.20        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30        35.38        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       32.71        19.27        18.84        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO 
       15.81        37.05        19.33        12.59        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        27.35        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88        77.33         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI 
        9.34        28.93        30.67        59.28        78.38        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       14.04        13.28         9.47        26.10        18.21        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       24.95        23.64        14.83         4.44        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       125.42                        225.50 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       22.390                        30.555 
[1] "0.6 - 125.4 (22.4)" "0.1 - 225.5 (30.6)"
[1] "hr=" "3.8"
D54V2, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    28  18
  DEL PEAK  4(2Q22.1) WILD-TYPE 262 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     28   18
  DEL PEAK  4(2Q22.1) WILD-TYPE  262  206
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                           28                           262
  YES                          18                           206
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                        19
  DEL PEAK  4(2Q22.1) WILD-TYPE                                     385
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  4(2Q22.1) MUTATED                               2
  DEL PEAK  4(2Q22.1) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                  28
  DEL PEAK  4(2Q22.1) WILD-TYPE                                85
D54V3, multiclass
                                         clus
vv                                        DEL PEAK  4(2Q22.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          19
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                28
                                         clus
vv                                        DEL PEAK  4(2Q22.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           385
  MIXED SEROUS AND ENDOMETRIOID                                      20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED    24   2   5  10
  DEL PEAK  4(2Q22.1) WILD-TYPE 347  20  11  30
D54V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                          24                           347
  R1                           2                            20
  R2                           5                            11
  RX                          10                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.3) MUTATED    39  12
  DEL PEAK  5(2Q37.3) WILD-TYPE 408  78
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           51                           486 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           12                            78 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-KP-A3VZ TCGA-A5-A0GR 
       18.08        20.81        27.09        66.41        23.74        36.82 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 
       36.33       118.19        34.16        18.90        22.26        17.06 
TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A0LI TCGA-AP-A3K1 
       21.21        16.87        16.87        63.91        97.71        21.90 
TCGA-AW-A1PO TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A1MS 
        0.56        76.83        30.12        43.82        20.52       102.31 
TCGA-BG-A18C TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A16G 
       15.45        61.87        92.88        83.64        29.95        27.42 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-DF-A2KS TCGA-DI-A1NO TCGA-E6-A1LZ 
       28.08        13.22         2.07       109.08         9.37        79.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A3AS TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ 
       10.92        49.15        34.39        16.34        54.15        23.90 
TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A3PV 
       17.62        15.81        11.08        29.10        14.70        41.56 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       38.70         8.19         4.44 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       10.19       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       80.38        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 
        1.81        19.79         4.44        47.84        16.93        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.21        22.78        17.88        10.19        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       36.00         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       31.99        33.07        66.15        28.64        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       25.51        14.96        11.21        18.41        20.25        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        21.14        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE 
       33.90         1.64        14.66        22.49        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        32.02        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       225.50        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        86.99        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
       15.88         4.27        18.84        17.29         2.20        71.61 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH 
      100.83        89.33        10.92        27.16        25.91        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        19.40        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        38.07        27.16        46.42        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        33.34        32.71        19.27        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       22.03        16.11        32.78        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       11.38        14.14        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        59.28        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        21.30 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       118.19                        225.50 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        27.09                         30.15 
[1] "0.6 - 118.2 (27.1)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.5"
D55V2, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED    27  22
  DEL PEAK  5(2Q37.3) WILD-TYPE 263 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     27   22
  DEL PEAK  5(2Q37.3) WILD-TYPE  263  202
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                           27                           263
  YES                          22                           202
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                        27
  DEL PEAK  5(2Q37.3) WILD-TYPE                                     377
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  5(2Q37.3) MUTATED                               2
  DEL PEAK  5(2Q37.3) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                  23
  DEL PEAK  5(2Q37.3) WILD-TYPE                                90
D55V3, multiclass
                                         clus
vv                                        DEL PEAK  5(2Q37.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          27
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                23
                                         clus
vv                                        DEL PEAK  5(2Q37.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           377
  MIXED SEROUS AND ENDOMETRIOID                                      20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.3) MUTATED    32   2   3   9
  DEL PEAK  5(2Q37.3) WILD-TYPE 339  20  13  31
D55V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                          32                           339
  R1                           2                            20
  R2                           3                            13
  RX                           9                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    57  21
  DEL PEAK  6(3P14.2) WILD-TYPE 390  69
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           78                           459 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           21                            69 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-2E-A9G8 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       41.06        57.80        67.66        36.39        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0YV 
       27.88         1.38        80.38        27.09        22.06        12.56 
TCGA-D1-A3JP TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 
       16.93        39.52        37.02        31.99        36.33        66.15 
TCGA-AJ-A23M TCGA-AJ-A2QN TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3TW 
       20.25        35.15        18.12         1.64        21.21        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       20.78        21.99       125.42        97.71        46.78        21.90 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3GI 
        0.56        37.78        76.83         4.77        71.24         0.39 
TCGA-B5-A0K3 TCGA-B5-A11I TCGA-B5-A1N2 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 
       27.29        75.72        31.36        15.45        22.39        31.00 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW 
       16.64        61.87        22.55        31.07        18.67         0.72 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QU 
        2.07        58.95        71.61        25.91        35.38        31.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A2CH TCGA-EO-A3KW TCGA-EY-A1GJ 
       79.10        10.92        49.15        19.40        16.34        23.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A2OQ TCGA-EY-A3L3 
       19.27        18.84        17.62        15.81        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       32.52        11.38        14.70        77.33         9.34        28.93 
TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A915 TCGA-SL-A6J9 
       30.67        17.75        26.10        18.21         8.19         0.07 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D 
       20.81        10.19       110.63        93.99        95.47        12.26 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       10.19        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN 
      112.54       105.37       123.68        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 
       42.35        15.95        31.99        33.07       118.19        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BD 
       14.43        10.26        21.14        19.79        34.36        34.16 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       18.90        33.90        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       16.87        22.32        12.82         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
      129.80        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        12.62        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       32.02        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        30.12        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       225.50       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
      136.60        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98        35.90        35.08 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        24.13        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
        8.48        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
      109.08       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        24.30         9.37        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        51.42        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX 
       38.07        27.16        46.42        26.96        22.26        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GS TCGA-EY-A1GT 
       23.34        23.34        33.34        32.71        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       32.78        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       20.05        45.76        31.04        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 
       39.88         7.99        25.22        96.69        59.01        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.56        78.38         1.74        14.04        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       23.24        21.30        38.70        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.07                          0.13 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       125.42                        225.50 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       26.005                        30.440 
[1] "0.1 - 125.4 (26.0)" "0.1 - 225.5 (30.4)"
[1] "hr=" "2.1"
D56V2, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    38  36
  DEL PEAK  6(3P14.2) WILD-TYPE 252 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     38   36
  DEL PEAK  6(3P14.2) WILD-TYPE  252  188
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                           38                           252
  YES                          36                           188
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                        29
  DEL PEAK  6(3P14.2) WILD-TYPE                                     375
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  6(3P14.2) MUTATED                               6
  DEL PEAK  6(3P14.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                  44
  DEL PEAK  6(3P14.2) WILD-TYPE                                69
D56V3, multiclass
                                         clus
vv                                        DEL PEAK  6(3P14.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          29
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                44
                                         clus
vv                                        DEL PEAK  6(3P14.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           375
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P14.2) MUTATED    55   3   4   7
  DEL PEAK  6(3P14.2) WILD-TYPE 316  19  12  33
D56V4, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  R0                          55                           316
  R1                           3                            19
  R2                           4                            12
  RX                           7                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK  7(3Q13.31) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(3Q13.31) MUTATED    35   8
  DEL PEAK  7(3Q13.31) WILD-TYPE 412  82
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            43                            494 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                             8                             82 
$`DEL PEAK  7(3Q13.31) MUTATED`
TCGA-AX-A2H8 TCGA-B5-A0JN TCGA-KP-A3VZ TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH 
       61.18        80.38        23.74        37.02        31.99        36.33 
TCGA-A5-A2K2 TCGA-AJ-A2QK TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 
      118.19        21.14        22.26        16.87        45.53       125.42 
TCGA-AP-A0LJ TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CA 
       46.72        46.78        36.13         0.56        37.78        32.02 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11W 
       20.52         0.30         0.30        27.85       185.79        19.50 
TCGA-B5-A5OD TCGA-BG-A3PP TCGA-BK-A0CB TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A16I 
       34.13        22.39        35.90        24.13        16.64        11.51 
TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DF-A2L0 TCGA-E6-A1LZ TCGA-EO-A3AS 
       18.67         2.07        18.84        25.91        79.10        34.39 
TCGA-EO-A3AZ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-H5-A2HR 
       27.16        19.27        18.84        29.10        77.33         1.74 
TCGA-QS-A8F1 
        4.44 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       18.08        20.81        10.19       110.63        57.80        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2HF 
       95.47        67.66        12.26        36.39        23.05        27.88 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        27.09        22.06        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
       16.93        33.30         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       13.84        73.32        36.00         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88       149.56        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       15.95        31.99        33.07        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       34.95        25.51        14.96        11.21        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       14.43        10.26        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        51.12        21.90        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       34.65        25.51        26.37        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 
       85.48        73.41        80.25        37.58         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G8 
        0.20         0.56        43.82         0.20         0.26         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       13.45        59.84       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       73.28        16.73        19.56        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       71.84        39.35        27.65        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.08        31.00        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR 
       58.95        15.88         4.27        17.29         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
      109.08       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10       110.10        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        19.40        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       23.90        33.34        32.71        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       11.38        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        21.30 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       38.70        22.59         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                          0.30                           0.07 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        185.79                         225.50 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                         27.16                          30.05 
[1] "0.3 - 185.8 (27.2)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.1"
D57V2, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED    22  17
  DEL PEAK  7(3Q13.31) WILD-TYPE 268 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED     22   17
  DEL PEAK  7(3Q13.31) WILD-TYPE  268  207
     clus
vv    DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  NO                            22                            268
  YES                           17                            207
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  7(3Q13.31) MUTATED                                        18
  DEL PEAK  7(3Q13.31) WILD-TYPE                                     386
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  7(3Q13.31) MUTATED                               3
  DEL PEAK  7(3Q13.31) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  7(3Q13.31) MUTATED                                  22
  DEL PEAK  7(3Q13.31) WILD-TYPE                                91
D57V3, multiclass
                                         clus
vv                                        DEL PEAK  7(3Q13.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           18
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 22
                                         clus
vv                                        DEL PEAK  7(3Q13.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            386
  MIXED SEROUS AND ENDOMETRIOID                                       19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  7(3Q13.31) MUTATED    28   1   0   4
  DEL PEAK  7(3Q13.31) WILD-TYPE 343  21  16  36
D57V4, multiclass
    clus
vv   DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  R0                           28                            343
  R1                            1                             21
  R2                            0                             16
  RX                            4                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK  8(4P16.3) MUTATION ANALYSIS
D58V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4P16.3) MUTATED    71  22
  DEL PEAK  8(4P16.3) WILD-TYPE 376  68
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           93                           444 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           22                            68 
$`DEL PEAK  8(4P16.3) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR 
       10.19       110.63        57.80        93.99        67.66        23.05 
TCGA-AX-A2HF TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A212 TCGA-EY-A214 
       27.88        66.41        12.56        16.93        10.19        14.40 
TCGA-KP-A3VZ TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A2K2 
       23.74       149.56        60.53        36.82        37.91       118.19 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A2QK TCGA-AJ-A3BD 
       28.64        25.51        14.96        18.41        21.14        34.16 
TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A05J 
        1.64        21.21        16.87        16.87        45.53        36.89 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA 
       33.40        21.90         0.56        37.78        34.65        32.02 
TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G4 
       25.91        30.12         2.96         0.23        20.52         0.30 
TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY 
       58.75        27.85        88.34        75.72        52.04        11.87 
TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V 
       22.39        24.13        61.87        92.88        83.64        39.48 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
       37.32        18.67         3.95        14.73        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.25        17.29        71.61       109.08        25.91        35.38 
TCGA-DI-A2QT TCGA-EO-A1Y7 TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GO 
       12.39        49.15        27.16        22.26        16.34        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR 
       18.84        17.62        20.05        45.76        27.35        11.38 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC 
       17.75        14.04        13.28         9.47        26.10        23.24 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       38.70         8.19         4.44 

$`DEL PEAK  8(4P16.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
       18.08        20.81        95.47        12.26        36.39        61.18 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        80.38        27.09        22.06        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       14.27         1.81        19.79         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
        6.21        22.78        17.88        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        36.00         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       39.52        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 
       31.99        31.99        36.33        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       34.95        11.21        20.25        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        18.12        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        22.26        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07        48.03        63.91        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       97.71        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12        36.13        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       32.91        25.51        26.37        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       73.41        80.25        37.58         4.77        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13        64.93         0.20         0.56        43.82         0.20 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY 
       56.91        86.37        55.30        59.24        86.01        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ 
       24.33        85.55        78.21         4.80        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY 
       11.15        24.30         2.33        22.92         1.41        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN 
        8.48        58.95        15.88         4.27        18.84         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30         9.37        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX 
       50.73        35.15        38.07        46.42        26.96        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GS 
       23.34        23.34        23.90        33.34        32.71        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 
       12.59        22.82        31.04        29.10        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-H5-A2HR TCGA-KP-A3W4 TCGA-PG-A6IB 
       25.22        96.69        59.01         1.74        18.21        21.30 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       149.56                        225.50 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                        25.51                         31.02 
[1] "0.2 - 149.6 (25.5)" "0.1 - 225.5 (31.0)"
[1] "hr=" "1.7"
D58V2, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    50  38
  DEL PEAK  8(4P16.3) WILD-TYPE 240 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     50   38
  DEL PEAK  8(4P16.3) WILD-TYPE  240  186
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  NO                           50                           240
  YES                          38                           186
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                        32
  DEL PEAK  8(4P16.3) WILD-TYPE                                     372
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  8(4P16.3) MUTATED                               6
  DEL PEAK  8(4P16.3) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                  56
  DEL PEAK  8(4P16.3) WILD-TYPE                                57
D58V3, multiclass
                                         clus
vv                                        DEL PEAK  8(4P16.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          32
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                56
                                         clus
vv                                        DEL PEAK  8(4P16.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           372
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4P16.3) MUTATED    65   4   4   8
  DEL PEAK  8(4P16.3) WILD-TYPE 306  18  12  32
D58V4, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  R0                          65                           306
  R1                           4                            18
  R2                           4                            12
  RX                           8                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK  9(4P15.31) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(4P15.31) MUTATED    73  25
  DEL PEAK  9(4P15.31) WILD-TYPE 374  65
  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                            98                            439 
  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                            25                             65 
$`DEL PEAK  9(4P15.31) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR 
       10.19       110.63        57.80        93.99        67.66        23.05 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A212 
       27.88         1.38        66.41        12.56        16.93        10.19 
TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR 
       14.40        23.74        39.52       149.56        60.53        36.82 
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK 
       37.91       118.19        28.64        25.51        14.96        18.41 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
       21.14        34.16         1.64        21.21        16.87        16.87 
TCGA-AP-A05H TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CA 
       45.53        33.40        21.90         0.56        37.78        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FS 
       25.91        76.83         4.77        30.12         2.96         0.23 
TCGA-AX-A3G1 TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY 
       20.52        58.75        27.85        75.72        52.04        11.87 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       29.65        34.13        34.95        22.39        35.08        24.13 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S 
       61.87        92.88        83.64        39.48        37.32        18.67 
TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS 
        3.95        14.73         0.72        17.29        71.61       109.08 
TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A3AS 
       25.91        35.38        12.39       110.10        49.15        34.39 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP 
       27.16        22.26        16.34        54.15        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       17.62        20.05        29.10        27.35        32.52        11.38 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.01         9.34        30.67        41.56        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
       13.28         9.47        26.10        18.21        23.24        38.70 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`DEL PEAK  9(4P15.31) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
       18.08        20.81        95.47        12.26        36.39        61.18 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
       80.38        27.09        22.06        61.87        51.55        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 
       66.77        13.84        73.32        36.00         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        65.75        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
       36.33        33.07        66.15        24.72        34.95        11.21 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        14.43        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.12        18.90        33.90        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       14.76        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        36.89        23.87        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        51.12        36.13        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       34.65        25.51        26.37        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.20         0.56        43.82         0.20         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       86.37        55.30        59.24        86.01        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       71.84        39.35        27.65        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        16.64        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       77.95        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41        13.22        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV 
       15.88         4.27        18.84         2.20       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        31.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       45.57        16.04         7.36        16.80        10.92        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        19.40        50.73        35.15        38.07        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       26.96        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       22.03        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 
       19.33        12.59        22.82        45.76        31.04        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       25.22        96.69        28.93        59.28        78.38         1.74 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        22.59        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                          0.23                           0.07 
  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                        149.56                         225.50 
  DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE 
                        26.005                         30.740 
[1] "0.2 - 149.6 (26.0)" "0.1 - 225.5 (30.7)"
[1] "hr=" "1.9"
D59V2, binary
                                cls
clus                               0   1
  DEL PEAK  9(4P15.31) MUTATED    52  41
  DEL PEAK  9(4P15.31) WILD-TYPE 238 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(4P15.31) MUTATED     52   41
  DEL PEAK  9(4P15.31) WILD-TYPE  238  183
     clus
vv    DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE
  NO                            52                            238
  YES                           41                            183
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  9(4P15.31) MUTATED                                        35
  DEL PEAK  9(4P15.31) WILD-TYPE                                     369
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  9(4P15.31) MUTATED                               5
  DEL PEAK  9(4P15.31) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  9(4P15.31) MUTATED                                  59
  DEL PEAK  9(4P15.31) WILD-TYPE                                54
D59V3, multiclass
                                         clus
vv                                        DEL PEAK  9(4P15.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           35
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 59
                                         clus
vv                                        DEL PEAK  9(4P15.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            369
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  9(4P15.31) MUTATED    63   4   5  10
  DEL PEAK  9(4P15.31) WILD-TYPE 308  18  11  30
D59V4, multiclass
    clus
vv   DEL PEAK  9(4P15.31) MUTATED DEL PEAK  9(4P15.31) WILD-TYPE
  R0                           63                            308
  R1                            4                             18
  R2                            5                             11
  RX                           10                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED    73  32
  DEL PEAK 10(4Q22.1) WILD-TYPE 374  58
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          105                           432 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           32                            58 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A2H8 
       29.39        10.19        57.80        93.99        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP 
       27.88         1.38        80.38        66.41        12.56        16.93 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       10.19        14.40         5.88        36.00        23.74        39.52 
TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG 
      149.56        65.75        60.53        36.82        37.91        31.99 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33       118.19        28.64        25.51        20.25        14.43 
TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 
       34.16         1.64        21.21        21.99        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA 
      125.42        97.71        33.40        37.78        25.51        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO 
       25.91        76.83         4.77        30.12         2.96        64.93 
TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A11I TCGA-B5-A11P 
        0.23        20.52         0.30         0.30        75.72        52.04 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 
      102.31        50.89        11.87        31.36        39.35        29.65 
TCGA-B5-A5OD TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 
       34.13        22.39        35.08        24.13        92.88        83.64 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU 
       39.48        37.32        18.67         3.95        14.73        13.22 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 
        4.27        18.84        17.29        71.61       109.08        25.91 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 
       35.38         9.37       110.10        51.42        27.16        26.96 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       22.26        54.15        32.71        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A2OO TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A2EY 
       22.03        45.76        32.52        68.38         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
       30.67        41.56        17.75        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A914 TCGA-PG-A915 
       23.24        22.59         8.19 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       20.81       110.63        95.47        67.66        12.26        36.39 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
       27.09        22.06        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       73.32         0.43        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       31.99        33.07        66.15        24.72        34.95        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        18.12        18.90        33.90        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.26        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.91        34.65        26.37        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT 
       46.49        38.24        17.75        30.74        31.13         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.20         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
      225.50        51.45        14.70        48.43        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        93.50        71.84        27.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98        35.90        31.00        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93        22.55         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KU 
       48.79         8.48        58.95        15.88         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30        12.39        31.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       38.07        46.42        16.34        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       33.34        16.11        32.78        15.81        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       19.33        12.59        22.82        20.05        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 
       27.35        11.38        14.14        14.70        16.96        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 
       77.33         7.99        25.22        96.69        59.01        59.28 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A7D5 
       78.38         1.74        14.04         9.47        21.30        38.70 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       149.56                        225.50 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        28.93                         30.05 
[1] "0.2 - 149.6 (28.9)" "0.1 - 225.5 (30.0)"
[1] "hr=" "2.3"
D60V2, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    54  45
  DEL PEAK 10(4Q22.1) WILD-TYPE 236 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     54   45
  DEL PEAK 10(4Q22.1) WILD-TYPE  236  179
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                           54                           236
  YES                          45                           179
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                        33
  DEL PEAK 10(4Q22.1) WILD-TYPE                                     371
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 10(4Q22.1) MUTATED                               6
  DEL PEAK 10(4Q22.1) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                  67
  DEL PEAK 10(4Q22.1) WILD-TYPE                                46
D60V3, multiclass
                                         clus
vv                                        DEL PEAK 10(4Q22.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          33
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                67
                                         clus
vv                                        DEL PEAK 10(4Q22.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           371
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED    64   6   7  10
  DEL PEAK 10(4Q22.1) WILD-TYPE 307  16   9  30
D60V4, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                          64                           307
  R1                           6                            16
  R2                           7                             9
  RX                          10                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 11(4Q34.3) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q34.3) MUTATED    95  34
  DEL PEAK 11(4Q34.3) WILD-TYPE 352  56
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          129                           408 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                           34                            56 
$`DEL PEAK 11(4Q34.3) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CR 
       29.39        20.81        10.19        57.80        93.99        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 
       61.18        27.88         1.38        80.38        27.09        66.41 
TCGA-BG-A0YV TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       12.56        10.19        14.40         5.88        36.00        23.74 
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       39.52       149.56        65.75        60.53        36.82        37.91 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       31.99        36.33       118.19        28.64        25.51        20.25 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       14.43        34.16         1.64        16.87        16.87        20.78 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO 
       21.99        45.53        48.79       125.42        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA 
       46.78        36.13         0.56        37.78        25.51        32.02 
TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 
       25.91         4.77        30.12        64.93         0.23        20.52 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
        0.30         0.39        27.85        75.72        52.04       102.31 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD 
       50.89        11.87        31.36        39.35        29.65        34.13 
TCGA-B5-A5OE TCGA-BG-A222 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD 
       34.95         9.57        22.39        35.08        24.13        16.64 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V 
        4.80        61.87        92.88        83.64        22.55        39.48 
TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K 
       37.32        31.07        18.67         3.95        14.73        28.08 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
       13.22         0.72        16.87         2.07         4.27        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A0WH TCGA-DI-A1NN TCGA-DI-A2QY 
       17.29        71.61       109.08        16.31        35.38       110.10 
TCGA-E6-A1LZ TCGA-EO-A22R TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ 
       79.10        61.74        51.42        19.40        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       26.96        22.26        16.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       17.62        22.03        45.76        29.10        27.35        32.52 
TCGA-EY-A54A TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       14.70         9.34        28.93        30.67        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
        1.74        17.75        26.10        18.21        23.24        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       22.59         8.19         4.44 

$`DEL PEAK 11(4Q34.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-BG-A0M6 
      110.63        95.47        67.66        12.26        36.39        22.06 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        51.55        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       47.84        16.93        33.30         6.21        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        17.92        19.89        66.77        13.84        73.32 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP 
       32.78       112.54       105.37       123.68        74.10        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       73.87        28.27        54.02        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ 
       33.07        66.15        24.72        34.95        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       18.41        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.12        18.90        33.90        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       15.95        14.76        22.32        12.82         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13       129.80        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12        21.90        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       32.91        34.65        26.37        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 
       31.13         0.20         0.56        43.82         0.20         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       225.50        51.45        14.70        48.43        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
      136.60        96.30        93.50        71.84        27.65        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       35.90        31.00        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        24.33        85.55        78.21        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        29.92        33.63        10.65         0.69 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O5 
        2.33        22.92         1.41        18.25        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
        2.20       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        49.15        37.71        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        51.52        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       46.42        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A548 
       12.59        22.82        20.05        31.04        11.38        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       96.69        59.01        59.28        14.04        13.28         9.47 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       21.30        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                       149.56                        225.50 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                        27.85                         30.74 
[1] "0.2 - 149.6 (27.9)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.1"
D61V2, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q34.3) MUTATED    67  55
  DEL PEAK 11(4Q34.3) WILD-TYPE 223 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q34.3) MUTATED     67   55
  DEL PEAK 11(4Q34.3) WILD-TYPE  223  169
     clus
vv    DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE
  NO                           67                           223
  YES                          55                           169
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 11(4Q34.3) MUTATED                                        45
  DEL PEAK 11(4Q34.3) WILD-TYPE                                     359
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 11(4Q34.3) MUTATED                               8
  DEL PEAK 11(4Q34.3) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 11(4Q34.3) MUTATED                                  77
  DEL PEAK 11(4Q34.3) WILD-TYPE                                36
D61V3, multiclass
                                         clus
vv                                        DEL PEAK 11(4Q34.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          45
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                77
                                         clus
vv                                        DEL PEAK 11(4Q34.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           359
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q34.3) MUTATED    82   6   8   9
  DEL PEAK 11(4Q34.3) WILD-TYPE 289  16   8  31
D61V4, multiclass
    clus
vv   DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE
  R0                          82                           289
  R1                           6                            16
  R2                           8                             8
  RX                           9                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 12(5Q12.1) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q12.1) MUTATED    79  31
  DEL PEAK 12(5Q12.1) WILD-TYPE 368  59
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          110                           427 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           31                            59 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A06B 
       41.06        29.39        20.81        10.19        93.99        67.66 
TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP 
       27.88        80.38        22.06        66.41        12.56        16.93 
TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       33.30        10.19        14.40        17.92        36.00        23.74 
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG 
       39.52       149.56        65.75        37.91        17.59        31.99 
TCGA-A5-A1OH TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A3BD 
       36.33        25.51        14.96        20.25        21.14        34.16 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H 
        1.64        22.26        21.21        16.87        16.87        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX 
       48.79       125.42        97.71        33.40        21.90        36.13 
TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 
       37.78        25.51        32.02        76.83         4.77        30.12 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
       43.82         0.20        20.52         0.30         0.26         0.39 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 
       27.85        75.72        50.89        31.36        39.35        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       34.13        34.95        22.39        35.08        31.00        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16N 
       16.64        92.88        83.64        39.48        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-DF-A2KR 
       18.67        14.73        13.22        18.25         2.07        71.61 
TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       25.91         9.37        31.10       110.10        79.10        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 
       49.15        37.71        51.42        34.39        27.16        26.96 
TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW 
       22.26        23.90        19.27        18.84        17.62        11.08 
TCGA-EY-A3QX TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       32.52        77.33        96.69        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A914 
       78.38        14.04         9.47        26.10        23.24        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AP-A053 
       88.18        60.53        30.15        16.83        18.08       110.63 
TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 
       57.80        95.47        12.26        36.39        23.05        61.18 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
        1.38        27.09        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       19.79         4.44        47.84         6.21        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        19.89         5.88        66.77        13.84        73.32 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        0.43        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN 
       32.78       112.54       105.37       123.68        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       31.99        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       34.95        11.21        18.41        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        18.12        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        36.89        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        34.65        26.37 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       25.91        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.56         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        73.64        61.68        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS 
       19.50        18.41        17.36        16.57       225.50       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       51.45        14.70        48.43        11.87        52.54       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       96.30        93.50        71.84        27.65        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 
       13.78        14.73        14.01        15.45        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       35.90        31.76        24.99        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41         0.72        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV 
       18.84        17.29         2.20       109.08       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       35.38        12.39        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.04         7.36        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.52        19.40        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       38.07        46.42        16.34        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        32.71        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       31.04        29.10        27.35        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       16.96        68.38        39.88         7.99        25.22        59.01 
TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W4 
        9.34        59.28         1.74        17.75        13.28        18.21 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        38.70        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       149.56                        225.50 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       27.865                        30.150 
[1] "0.2 - 149.6 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.2"
D62V2, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    52  51
  DEL PEAK 12(5Q12.1) WILD-TYPE 238 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     52   51
  DEL PEAK 12(5Q12.1) WILD-TYPE  238  173
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                           52                           238
  YES                          51                           173
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                        37
  DEL PEAK 12(5Q12.1) WILD-TYPE                                     367
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 12(5Q12.1) MUTATED                               4
  DEL PEAK 12(5Q12.1) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                  70
  DEL PEAK 12(5Q12.1) WILD-TYPE                                43
D62V3, multiclass
                                         clus
vv                                        DEL PEAK 12(5Q12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          37
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                70
                                         clus
vv                                        DEL PEAK 12(5Q12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           367
  MIXED SEROUS AND ENDOMETRIOID                                      18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED    69   4   4  11
  DEL PEAK 12(5Q12.1) WILD-TYPE 302  18  12  29
D62V4, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                          69                           302
  R1                           4                            18
  R2                           4                            12
  RX                          11                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D63V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED    33  12
  DEL PEAK 13(6Q26) WILD-TYPE 414  78
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         45                         492 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         12                          78 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-BG-A0YV TCGA-E6-A8L9 
       29.39        10.19        61.18         1.38        12.56        33.30 
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-AJ-A23N TCGA-AJ-A3BF 
      149.56        60.53        37.91        36.33        14.43        18.12 
TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AW-A1PO TCGA-AX-A0IW 
        1.64        16.87        36.89       125.42         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2IO TCGA-B5-A11P TCGA-B5-A1MU 
       34.65        37.58         4.77        64.93        52.04        50.89 
TCGA-B5-A1MY TCGA-BG-A3PP TCGA-BS-A0V6 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16J 
       11.87        22.39        89.59        22.55        11.51        29.92 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y8 TCGA-EO-A22X 
        4.27        17.29       110.10        79.10        37.71        57.60 
TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A3PV 
       34.39        26.96        29.10        11.38        77.33        41.56 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-PG-A7D5 
        1.74        13.28        38.70 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB 
       12.26        36.39        23.05        27.88        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
       22.06        66.41        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        16.93         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       17.88        10.19        14.40        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
        5.88        66.77        13.84        73.32        36.00        23.74 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
        0.43        39.52        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 
       42.35        15.95        31.99        31.99        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        18.41        20.25        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       35.15        34.36        34.16        18.90        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       225.50       102.31        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.13        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16N TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KN 
       48.79         8.48        58.95        15.88        18.84         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       25.91        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        12.39        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       19.40        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       32.52        14.14        14.70        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        25.22        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       30.67        59.28        78.38        17.75        14.04         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        21.30        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.56                        0.07 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     149.56                      225.50 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     33.300                      29.785 
[1] "0.6 - 149.6 (33.3)" "0.1 - 225.5 (29.8)"
[1] "hr=" "1.6"
D63V2, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    17  25
  DEL PEAK 13(6Q26) WILD-TYPE 273 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     17   25
  DEL PEAK 13(6Q26) WILD-TYPE  273  199
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                         17                         273
  YES                        25                         199
[1] 2 2
[1] FALSE
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                        13
  DEL PEAK 13(6Q26) WILD-TYPE                                     391
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 13(6Q26) MUTATED                               3
  DEL PEAK 13(6Q26) WILD-TYPE                            19
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                  30
  DEL PEAK 13(6Q26) WILD-TYPE                                83
D63V3, multiclass
                                         clus
vv                                        DEL PEAK 13(6Q26) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        13
  MIXED SEROUS AND ENDOMETRIOID                                   3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              30
                                         clus
vv                                        DEL PEAK 13(6Q26) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         391
  MIXED SEROUS AND ENDOMETRIOID                                    19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(6Q26) MUTATED    35   1   1   2
  DEL PEAK 13(6Q26) WILD-TYPE 336  21  15  38
D63V4, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  R0                        35                         336
  R1                         1                          21
  R2                         1                          15
  RX                         2                          38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 14(7P22.3) MUTATION ANALYSIS
D64V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7P22.3) MUTATED    49  22
  DEL PEAK 14(7P22.3) WILD-TYPE 398  68
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           71                           466 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           22                            68 
$`DEL PEAK 14(7P22.3) MUTATED`
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0KB 
      110.63        93.99        67.66        23.05         1.38        27.09 
TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A214 TCGA-KP-A3VZ TCGA-A5-A0R6 TCGA-A5-A1OH 
       33.30        10.19        14.40        23.74        37.91        36.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AP-A054 TCGA-AP-A05H 
       14.96        20.25         1.64        16.87        23.31        45.53 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW 
       48.79        97.71        46.78        21.90         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.65        32.02         4.77        30.12        30.74         2.96 
TCGA-AX-A2IO TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1N2 TCGA-BG-A3PP 
       64.93        27.29        27.85        75.72        31.36        22.39 
TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A16I TCGA-D1-A16V 
       35.08        16.64        92.88        29.95        11.51         3.95 
TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO 
        0.72        58.95        71.61        25.91        35.38         9.37 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
      110.10        79.10        16.04        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-FI-A2CY TCGA-FI-A2EW 
       34.39        22.26        45.76        29.10        68.38        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
        1.74        13.28        23.24        38.70         8.19 

$`DEL PEAK 14(7P22.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D 
       18.08        20.81        10.19        57.80        95.47        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 
       36.39        61.18        27.88        80.38        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        16.93         6.21        22.78        17.88 
TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       18.87        17.92        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       31.99        31.99        33.07       118.19        66.15        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       24.72        34.95        25.51        11.21        18.41        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.12        18.90        33.90        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        21.99        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        36.89        23.87        12.62        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       51.12        36.13        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       80.25        37.58        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       46.49        38.24        17.75        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       54.44        73.64        61.68        85.78        52.04        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        48.43        11.87        52.54       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98        35.90        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       63.58        83.64        86.99        66.48        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
        8.48        15.88         4.27        18.84        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
      109.08       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
       58.95         2.37        45.57         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       12.59        22.82        20.05        31.04        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 
       11.38        14.14        14.70        16.96        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
        7.99        25.22        96.69        17.75        14.04         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       26.10        18.21        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                       110.63                        225.50 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                       30.120                        29.785 
[1] "0.6 - 110.6 (30.1)" "0.1 - 225.5 (29.8)"
[1] "hr=" "2.2"
D64V2, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED    41  26
  DEL PEAK 14(7P22.3) WILD-TYPE 249 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED     41   26
  DEL PEAK 14(7P22.3) WILD-TYPE  249  198
     clus
vv    DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  NO                           41                           249
  YES                          26                           198
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 14(7P22.3) MUTATED                                        23
  DEL PEAK 14(7P22.3) WILD-TYPE                                     381
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 14(7P22.3) MUTATED                               5
  DEL PEAK 14(7P22.3) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 14(7P22.3) MUTATED                                  44
  DEL PEAK 14(7P22.3) WILD-TYPE                                69
D64V3, multiclass
                                         clus
vv                                        DEL PEAK 14(7P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          23
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                44
                                         clus
vv                                        DEL PEAK 14(7P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           381
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(7P22.3) MUTATED    46   4   4   9
  DEL PEAK 14(7P22.3) WILD-TYPE 325  18  12  31
D64V4, multiclass
    clus
vv   DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  R0                          46                           325
  R1                           4                            18
  R2                           4                            12
  RX                           9                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = DEL PEAK 15(7Q11.22) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(7Q11.22) MUTATED    33   8
  DEL PEAK 15(7Q11.22) WILD-TYPE 414  82
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            41                            496 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                             8                             82 
$`DEL PEAK 15(7Q11.22) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-B5-A0JN TCGA-B5-A0KB TCGA-EY-A212 
       10.19        93.99        23.05        80.38        27.09        10.19 
TCGA-EY-A547 TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3TW 
       17.92        37.91        36.33       118.19        34.16        16.87 
TCGA-AP-A05H TCGA-AX-A1CA TCGA-AX-A2HK TCGA-AX-A2IO TCGA-B5-A11I TCGA-BG-A3PP 
       45.53        32.02         2.96        64.93        75.72        22.39 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16S 
       35.08        31.00        16.64        92.88        39.48        18.67 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN 
        2.07        58.95        18.84        71.61        25.91        35.38 
TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A2OO TCGA-EY-A2OQ 
       79.10        19.40        22.26        54.15        45.76        29.10 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       96.69        59.01        59.28        41.56        78.38 

$`DEL PEAK 15(7Q11.22) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        20.81       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 
       12.26        36.39        61.18        27.88         1.38        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       66.41        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
       19.79         4.44        47.84        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        14.40        18.87        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK 
       19.79        35.15        34.36        18.12        18.90        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        36.89        23.87        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.86        27.85        51.12        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       26.37        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       48.43        11.87        52.54        31.36       136.60        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       93.50        71.84        39.35        27.65        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       15.45        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       11.31        35.90        34.98        35.90        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS 
        8.48        15.88         4.27        17.29         2.20       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.62        22.03        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       20.05        31.04        27.35        32.52        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI 
       25.22         9.34        28.93        30.67         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       14.04        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       21.30        38.70        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                          2.07                           0.07 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                        118.19                         225.50 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                         35.38                          29.36 
[1] "2.1 - 118.2 (35.4)" "0.1 - 225.5 (29.4)"
[1] "hr=" "1"  
D65V2, binary
                                cls
clus                               0   1
  DEL PEAK 15(7Q11.22) MUTATED    23  17
  DEL PEAK 15(7Q11.22) WILD-TYPE 267 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(7Q11.22) MUTATED     23   17
  DEL PEAK 15(7Q11.22) WILD-TYPE  267  207
     clus
vv    DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE
  NO                            23                            267
  YES                           17                            207
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 15(7Q11.22) MUTATED                                        15
  DEL PEAK 15(7Q11.22) WILD-TYPE                                     389
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 15(7Q11.22) MUTATED                               2
  DEL PEAK 15(7Q11.22) WILD-TYPE                            20
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 15(7Q11.22) MUTATED                                  24
  DEL PEAK 15(7Q11.22) WILD-TYPE                                89
D65V3, multiclass
                                         clus
vv                                        DEL PEAK 15(7Q11.22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           15
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 24
                                         clus
vv                                        DEL PEAK 15(7Q11.22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            389
  MIXED SEROUS AND ENDOMETRIOID                                       20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 15(7Q11.22) MUTATED    29   3   2   4
  DEL PEAK 15(7Q11.22) WILD-TYPE 342  19  14  36
D65V4, multiclass
    clus
vv   DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE
  R0                           29                            342
  R1                            3                             19
  R2                            2                             14
  RX                            4                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = DEL PEAK 16(7Q31.1) MUTATION ANALYSIS
D66V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(7Q31.1) MUTATED    39  16
  DEL PEAK 16(7Q31.1) WILD-TYPE 408  74
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           55                           482 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           16                            74 
$`DEL PEAK 16(7Q31.1) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A1CR TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0YV 
       10.19        57.80        23.05        80.38        22.06        12.56 
TCGA-EY-A212 TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A23N 
       10.19        37.91        36.33       118.19        20.25        14.43 
TCGA-AJ-A3BD TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A2HK TCGA-B5-A11I 
       34.16        46.78        37.78        32.02         2.96        75.72 
TCGA-B5-A1MY TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 
       11.87        22.39        35.08        31.00        24.13        92.88 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 
       22.55        39.48        18.67        13.22        18.25         2.07 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A2QY 
       58.95        18.84       109.08        25.91        35.38       110.10 
TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A2ON 
       79.10        19.40        26.96        22.26        54.15        20.05 
TCGA-EY-A2OO TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 
       45.76        11.38        14.70        96.69        59.01        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       41.56        78.38        23.24        38.70        22.59         8.19 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 16(7Q31.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08        20.81       110.63        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB 
       12.26        36.39        61.18        27.88         1.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       17.88        14.40        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E 
       66.77        13.84        73.32        36.00        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       66.15        28.64        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        18.12        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        32.91        34.65        25.51        26.37        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       27.29        57.76        64.21        63.55        27.85        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       59.84       185.79       113.36        88.34        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       52.54        31.36       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       39.35        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       34.98        35.90        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       28.67        23.93         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        0.72        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN 
       48.79         8.48        15.88         4.27        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
       71.61       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW 
       50.73        35.15        38.07        27.16        46.42        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OP 
       11.08        37.05        19.33        12.59        22.82        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       29.10        27.35        32.52        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88        77.33         7.99        25.22         9.34        28.93 
TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       30.67         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       26.10        18.21        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                         0.07                          0.13 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                       118.19                        225.50 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                       26.960                        29.935 
[1] "0.1 - 118.2 (27.0)" "0.1 - 225.5 (29.9)"
[1] "hr=" "1.9"
D66V2, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED    25  28
  DEL PEAK 16(7Q31.1) WILD-TYPE 265 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED     25   28
  DEL PEAK 16(7Q31.1) WILD-TYPE  265  196
     clus
vv    DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  NO                           25                           265
  YES                          28                           196
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 16(7Q31.1) MUTATED                                        12
  DEL PEAK 16(7Q31.1) WILD-TYPE                                     392
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 16(7Q31.1) MUTATED                               3
  DEL PEAK 16(7Q31.1) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 16(7Q31.1) MUTATED                                  40
  DEL PEAK 16(7Q31.1) WILD-TYPE                                73
D66V3, multiclass
                                         clus
vv                                        DEL PEAK 16(7Q31.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          12
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                40
                                         clus
vv                                        DEL PEAK 16(7Q31.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           392
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(7Q31.1) MUTATED    37   2   3   8
  DEL PEAK 16(7Q31.1) WILD-TYPE 334  20  13  32
D66V4, multiclass
    clus
vv   DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  R0                          37                           334
  R1                           2                            20
  R2                           3                            13
  RX                           8                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = DEL PEAK 17(7Q36.1) MUTATION ANALYSIS
D67V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q36.1) MUTATED    42  21
  DEL PEAK 17(7Q36.1) WILD-TYPE 405  69
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           63                           474 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           21                            69 
$`DEL PEAK 17(7Q36.1) MUTATED`
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CR TCGA-B5-A0JN 
       10.19       110.63        57.80        93.99        23.05        80.38 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A221 TCGA-EY-A212 TCGA-A5-A0G5 TCGA-A5-A0R6 
       22.06        12.56         1.81        10.19        37.02        37.91 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       31.99        36.33       118.19        20.25        14.43        34.16 
TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A1DQ TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1CA 
      125.42        36.36        46.78        35.74        34.65        32.02 
TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-B5-A11I TCGA-B5-A1MY TCGA-BG-A3PP TCGA-BK-A0CC 
        4.77         2.96        75.72        11.87        22.39        35.08 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S 
       31.00        24.13        92.88        22.55        39.48        18.67 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DF-A2L0 
       13.22        18.25         2.07        58.95        18.84        25.91 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG TCGA-EO-A2CH 
       35.38         9.37       110.10        79.10        51.42        19.40 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A4KR 
       26.96        22.26        54.15        20.05        45.76        11.38 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W3 
       96.69        59.01        59.28        41.56        78.38        26.10 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       23.24        38.70         8.19 

$`DEL PEAK 17(7Q36.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3IA TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
       18.08        20.81        95.47        67.66        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS 
       61.18        27.88         1.38        27.09        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP 
       51.55        14.27        19.79         4.44        47.84        16.93 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 
       33.30         6.21        22.78        17.88        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
      149.56        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      123.68        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       36.82        28.27        54.02        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       33.07        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96        11.21        18.41        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       35.15        34.36        18.12        18.90        33.90         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ 
       48.79       117.99       110.37        66.25        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       51.12        21.90        36.13         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       32.91        25.51        26.37        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       51.45        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
       96.30        93.50        71.84        39.35        27.65        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       20.12        11.31        35.90        34.98        35.90        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41         0.72        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA 
       15.06         1.05         3.95        48.79         8.48        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
        4.27        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30        12.39        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.52        34.39        50.73        35.15        38.07        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       46.42        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       32.71        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       22.82        31.04        29.10        27.35        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI 
       25.22         9.34        28.93        30.67         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
       14.04        13.28         9.47        18.21        21.30        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                         1.81                          0.07 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                       125.42                        225.50 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                        32.02                         29.67 
[1] "1.8 - 125.4 (32.0)" "0.1 - 225.5 (29.7)"
[1] "hr=" "2.1"
D67V2, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED    31  31
  DEL PEAK 17(7Q36.1) WILD-TYPE 259 193
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED     31   31
  DEL PEAK 17(7Q36.1) WILD-TYPE  259  193
     clus
vv    DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  NO                           31                           259
  YES                          31                           193
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 17(7Q36.1) MUTATED                                        13
  DEL PEAK 17(7Q36.1) WILD-TYPE                                     391
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 17(7Q36.1) MUTATED                               4
  DEL PEAK 17(7Q36.1) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 17(7Q36.1) MUTATED                                  46
  DEL PEAK 17(7Q36.1) WILD-TYPE                                67
D67V3, multiclass
                                         clus
vv                                        DEL PEAK 17(7Q36.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          13
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                46
                                         clus
vv                                        DEL PEAK 17(7Q36.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           391
  MIXED SEROUS AND ENDOMETRIOID                                      18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(7Q36.1) MUTATED    44   2   4   7
  DEL PEAK 17(7Q36.1) WILD-TYPE 327  20  12  33
D67V4, multiclass
    clus
vv   DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  R0                          44                           327
  R1                           2                            20
  R2                           4                            12
  RX                           7                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED    82  35
  DEL PEAK 18(8P23.2) WILD-TYPE 365  55
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          117                           420 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           35                            55 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CP TCGA-AX-A2HF 
       41.06        20.81        57.80        93.99        36.39        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-EY-A212 
        1.38        80.38        27.09        22.06        66.41        10.19 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ 
       14.40        17.92         5.88        23.74        39.52        65.75 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A7WK TCGA-AJ-A23M 
       31.99        36.33        66.15        28.64        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A05J 
       14.43        21.21        16.87        16.87        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO 
       48.79       125.42        97.71        46.78        21.90         0.56 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CN TCGA-AX-A2H2 
       37.78        34.65        32.02        25.91        37.58         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HH TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3GI 
       30.12        71.24        17.75        43.82         0.30         0.39 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY 
       27.29        27.85        75.72       225.50       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0MT TCGA-BG-A0YU 
       31.36        29.65        34.13        34.95        21.17        14.83 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 
       23.70        22.39        31.00        24.13        61.87        92.88 
TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S 
       29.95        22.55        39.48        27.42        11.51        18.67 
TCGA-D1-A16V TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ 
        3.95        13.22         0.72        58.95        18.84        17.29 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       71.61       109.08        35.38         9.37        12.39       110.10 
TCGA-EO-A1Y7 TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KU 
       49.15        57.60        51.42        34.39        27.16        22.26 
TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       23.90        22.03        15.81        20.05        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       32.52        11.38        14.70        77.33        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
        9.34        28.93        41.56        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
       14.04        13.28         9.47        18.21        23.24        38.70 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       22.59         8.19         4.44 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CR 
       10.19       110.63        95.47        67.66        12.26        23.05 
TCGA-AX-A2H8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       61.18        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
       19.79         4.44        47.84        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       22.78        17.88        18.87        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32        36.00         0.43        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      123.68        74.10        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       33.07       118.19        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       11.21        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.16        18.12        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        22.26        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07        48.03        63.91        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        25.51        26.37 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H7 
       34.09        76.83        85.48        73.41        80.25        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       81.37        34.32        46.49        38.24        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       18.41        17.36        16.57        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       39.35        27.65        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.83        56.58        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
       15.45         9.57        20.02        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98        35.90        35.08        31.76        24.99        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       23.93         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16N 
       37.32        36.36        37.51        36.79        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       22.92         1.41        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA 
       15.06         1.05         3.95        48.79         8.48        15.88 
TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         2.20       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU 
       25.91        16.31        39.29        36.62        24.30        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       66.90        46.26        51.52        19.40        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        46.42        26.96        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        33.34        32.71        19.27        18.84        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        11.08        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       22.82        45.76        31.04        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-KP-A3W3 
       39.88         7.99        25.22        30.67        59.28        26.10 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       21.30        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         0.30                          0.07 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       225.50                        185.79 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        27.35                         30.74 
[1] "0.3 - 225.5 (27.4)" "0.1 - 185.8 (30.7)"
[1] "hr=" "2.5"
D68V2, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    58  52
  DEL PEAK 18(8P23.2) WILD-TYPE 232 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     58   52
  DEL PEAK 18(8P23.2) WILD-TYPE  232  172
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                           58                           232
  YES                          52                           172
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                        36
  DEL PEAK 18(8P23.2) WILD-TYPE                                     368
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 18(8P23.2) MUTATED                               6
  DEL PEAK 18(8P23.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                  77
  DEL PEAK 18(8P23.2) WILD-TYPE                                36
D68V3, multiclass
                                         clus
vv                                        DEL PEAK 18(8P23.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          36
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                77
                                         clus
vv                                        DEL PEAK 18(8P23.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           368
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED    71   5   7  13
  DEL PEAK 18(8P23.2) WILD-TYPE 300  17   9  27
D68V4, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                          71                           300
  R1                           5                            17
  R2                           7                             9
  RX                          13                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = DEL PEAK 19(8P21.2) MUTATION ANALYSIS
D69V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(8P21.2) MUTATED    83  33
  DEL PEAK 19(8P21.2) WILD-TYPE 364  57
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          116                           421 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                           33                            57 
$`DEL PEAK 19(8P21.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A1CP TCGA-AX-A2HF 
       41.06        20.81        57.80        93.99        36.39        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-EY-A212 
        1.38        80.38        27.09        22.06        66.41        10.19 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ 
       14.40        17.92         5.88        23.74        39.52        65.75 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A7WK 
       31.99        36.33       118.19        66.15        28.64        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H 
       20.25        14.43        21.21        16.87        16.87        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       36.89        48.79       125.42        97.71        46.78        21.90 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
        0.56        37.78        34.65        25.51        32.02        25.91 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A3G4 TCGA-AX-A3GI 
       37.58         4.77        30.12        71.24         0.30         0.39 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY 
       27.29        27.85        75.72       225.50       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0MT TCGA-BG-A2AE 
       31.36        29.65        34.13        34.95        21.17        23.70 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZP 
       22.39        31.00        24.13        61.87        92.88        29.95 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 
       22.55        39.48        27.42        11.51        18.67        14.73 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR 
       13.22         0.72        58.95        18.84        17.29        71.61 
TCGA-DF-A2KS TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A22X 
      109.08        35.38        12.39       110.10        37.71        57.60 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GJ 
       51.42        34.39        27.16        26.96        22.26        23.90 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.03        15.81        20.05        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       11.38        68.38        77.33        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.93        41.56        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       13.28         9.47        18.21        23.24        38.70        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`DEL PEAK 19(8P21.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CR 
       10.19       110.63        95.47        67.66        12.26        23.05 
TCGA-AX-A2H8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       61.18        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 
       19.79         4.44        47.84        16.93        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       22.78        17.88        18.87        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32        36.00         0.43        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      123.68        74.10        60.53        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        54.02        23.21        68.65        37.91        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ 
       33.07        24.72        34.95        25.51        14.96        11.21 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26        21.14        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       18.12        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.26        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       35.11         0.13       129.80        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       48.03        63.91        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX 
        6.71        60.23        45.86        27.85        51.12        36.13 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF 
       77.39        13.28        32.91        26.37        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       85.48        73.41        80.25        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       88.34        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       18.41        17.36        16.57        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       39.35        27.65        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45        15.45         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       86.99        66.48        16.83         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       28.67        23.93         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J 
       36.10        37.32        36.36        37.51        36.79        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       15.88         4.27         2.20       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        31.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       45.57        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CH 
       61.74        61.55        66.90        46.26        51.52        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX 
       50.73        35.15        38.07        46.42        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        33.34        32.71        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        16.11        32.78        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A 
       12.59        22.82        45.76        31.04        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2F8 TCGA-FI-A2F9 
       16.96        39.88         7.99        25.22        30.67        59.28 
TCGA-KP-A3W3 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       26.10        21.30        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                         0.30                          0.07 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                       225.50                        185.79 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                       27.635                        30.670 
[1] "0.3 - 225.5 (27.6)" "0.1 - 185.8 (30.7)"
[1] "hr=" "2.2"
D69V2, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P21.2) MUTATED    58  51
  DEL PEAK 19(8P21.2) WILD-TYPE 232 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P21.2) MUTATED     58   51
  DEL PEAK 19(8P21.2) WILD-TYPE  232  173
     clus
vv    DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE
  NO                           58                           232
  YES                          51                           173
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 19(8P21.2) MUTATED                                        28
  DEL PEAK 19(8P21.2) WILD-TYPE                                     376
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 19(8P21.2) MUTATED                               7
  DEL PEAK 19(8P21.2) WILD-TYPE                            15
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 19(8P21.2) MUTATED                                  82
  DEL PEAK 19(8P21.2) WILD-TYPE                                31
D69V3, multiclass
                                         clus
vv                                        DEL PEAK 19(8P21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          28
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                82
                                         clus
vv                                        DEL PEAK 19(8P21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           376
  MIXED SEROUS AND ENDOMETRIOID                                      15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P21.2) MUTATED    72   5   7  11
  DEL PEAK 19(8P21.2) WILD-TYPE 299  17   9  29
D69V4, multiclass
    clus
vv   DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE
  R0                          72                           299
  R1                           5                            17
  R2                           7                             9
  RX                          11                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = DEL PEAK 20(9P23) MUTATION ANALYSIS
D70V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(9P23) MUTATED    56  24
  DEL PEAK 20(9P23) WILD-TYPE 391  66
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         80                         457 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         24                          66 
$`DEL PEAK 20(9P23) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-E6-A8L9 
       20.81        10.19        27.09        66.41        16.93        33.30 
TCGA-EY-A214 TCGA-EY-A72D TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GG TCGA-A5-A0GR 
       14.40         5.88        39.52       149.56       123.68        36.82 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO 
       37.91        17.59        42.35        36.33        28.64        25.51 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       20.25        14.43        34.16        18.12        18.90         1.64 
TCGA-AJ-A3I9 TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ 
       17.06        20.78        45.53        48.79        97.71        46.78 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF 
       21.90         0.56        37.78        34.65        25.51        76.83 
TCGA-AX-A2H2 TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-B5-A0K8 TCGA-B5-A11P 
        4.77        43.82         0.30         0.26        27.85        52.04 
TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BK-A0CC 
      102.31       136.60        39.35        34.95        15.45        35.08 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 
       31.00        16.64        83.64        22.55        39.48        37.32 
TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.67         2.07        17.29        71.61        25.91        35.38 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 
       12.39       110.10        49.15        51.42        27.16        26.96 
TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EX 
       19.27        22.03        11.38        14.70        77.33         9.34 
TCGA-FI-A2EY TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC 
       28.93        17.75        14.04         9.47        26.10        23.24 
TCGA-PG-A7D5 TCGA-QS-A8F1 
       38.70         4.44 

$`DEL PEAK 20(9P23) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       18.08       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       12.26        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       80.38        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
        1.81        19.79         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX 
       17.88        10.19        18.87        17.92        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5S-A9Q8 
       13.84        73.32        36.00        23.74         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37        74.10        65.75        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K2 
       29.06        15.95        31.99        31.99        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       66.15        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK 
       10.26        21.14        19.79        35.15        34.36        33.90 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        22.26        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
       21.99        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S 
       60.23        45.86        27.85        51.12        36.13        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        61.08        35.74        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        32.91        26.37        32.02        25.91        34.09 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56         0.20        20.52         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      225.50        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       52.54        31.36        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       11.31        22.39        35.90        34.98        35.90        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        24.13        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       24.33        85.55        78.21         4.80        77.95        61.87 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA 
       67.99        96.49        30.74        97.41        92.88       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       89.59        63.58        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KS 
       58.95        15.88         4.27        18.84         2.20       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30         9.37        31.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        46.42        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        23.90        33.34        32.71        18.84        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
       27.35        32.52        14.14        16.96        68.38        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 
        7.99        25.22        96.69        59.01        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB 
       41.56        78.38         1.74        13.28        18.21        21.30 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       22.59         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                       0.26                        0.07 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                     149.56                      225.50 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                     27.025                      30.150 
[1] "0.3 - 149.6 (27.0)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.2"
D70V2, binary
                             cls
clus                            0   1
  DEL PEAK 20(9P23) MUTATED    41  36
  DEL PEAK 20(9P23) WILD-TYPE 249 188
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(9P23) MUTATED     41   36
  DEL PEAK 20(9P23) WILD-TYPE  249  188
     clus
vv    DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  NO                         41                         249
  YES                        36                         188
[1] 2 2
[1] FALSE
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 20(9P23) MUTATED                                        30
  DEL PEAK 20(9P23) WILD-TYPE                                     374
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 20(9P23) MUTATED                               4
  DEL PEAK 20(9P23) WILD-TYPE                            18
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 20(9P23) MUTATED                                  46
  DEL PEAK 20(9P23) WILD-TYPE                                67
D70V3, multiclass
                                         clus
vv                                        DEL PEAK 20(9P23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        30
  MIXED SEROUS AND ENDOMETRIOID                                   4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              46
                                         clus
vv                                        DEL PEAK 20(9P23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         374
  MIXED SEROUS AND ENDOMETRIOID                                    18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(9P23) MUTATED    50   3   5   8
  DEL PEAK 20(9P23) WILD-TYPE 321  19  11  32
D70V4, multiclass
    clus
vv   DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  R0                        50                         321
  R1                         3                          19
  R2                         5                          11
  RX                         8                          32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = DEL PEAK 21(9Q21.2) MUTATION ANALYSIS
D71V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(9Q21.2) MUTATED    90  39
  DEL PEAK 21(9Q21.2) WILD-TYPE 357  51
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          129                           408 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                           39                            51 
$`DEL PEAK 21(9Q21.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B 
       41.06        20.81        10.19       110.63        57.80        67.66 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB 
       36.39        23.05        61.18        27.88        80.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A3JP TCGA-E6-A8L9 
       22.06        66.41        12.56         1.81        16.93        33.30 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GG 
       10.19        14.40        17.92        23.74        39.52       123.68 
TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K2 
       36.82        37.91        17.59        42.35        36.33       118.19 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD 
       28.64        25.51        20.25        21.14        35.15        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3TW 
       18.12        18.90         1.64        22.26        17.06        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       20.78        21.99        45.53        48.79       125.42        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF 
       46.78        21.90        36.13        37.78        34.65        76.83 
TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       30.12         2.96         0.23        43.82        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
        0.26         0.39        27.85        75.72        52.04       102.31 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
       50.89        11.87        31.36       136.60        39.35        29.65 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       34.95        15.45        35.08        31.00        24.13        16.64 
TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 
       61.87        83.64         8.55        22.55        39.48        37.32 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW 
       31.07        18.67         3.95        28.08        13.22         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN 
        2.07        18.84        17.29        71.61        25.91        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        9.37        12.39       110.10        79.10        49.15        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC 
       51.42        19.40        27.16        26.96        16.34        54.15 
TCGA-EY-A1GO TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ 
       19.27        15.81        11.08        12.59        20.05        29.10 
TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       11.38        68.38        77.33        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       78.38        17.75        14.04        26.10        18.21        23.24 
TCGA-PG-A914 TCGA-QS-A8F1 TCGA-SL-A6J9 
       22.59         4.44         0.07 

$`DEL PEAK 21(9Q21.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A3G3 TCGA-BG-A0MS TCGA-BG-A0VT 
       93.99        95.47        12.26         1.38        61.87        51.55 
TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
       14.27        19.79         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        18.87        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32        36.00         0.43        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       74.10        65.75        60.53        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       54.02        23.21        68.65        19.59        24.62        29.06 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95        31.99        31.99        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O 
       34.95        14.96        11.21        18.41        14.43        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       19.79        34.36        33.90        14.66        22.49        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       16.87        22.32        12.82         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
      129.80        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.62        20.91       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12         0.56        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       32.91        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       30.74        31.13        64.93         0.20         0.56         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       225.50        51.45        14.70        48.43        52.54 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        93.50        71.84        27.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       14.83        13.78        14.73        14.01        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98        35.90        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
       29.95         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92         1.41        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KS 
        8.48        58.95        15.88         4.27         2.20       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        31.10        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
       45.57        16.04         7.36        16.80        10.92        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        51.52        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX 
       50.73        35.15        38.07        46.42        22.26        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       23.34        23.90        33.34        32.71        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       22.03        16.11        32.78        37.05        19.33        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A 
       45.76        31.04        27.35        32.52        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       16.96        39.88         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB 
        9.34        59.28         1.74        13.28         9.47        21.30 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       38.70         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       24.95        23.64        14.83        20.75        18.28         0.23 

  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                         0.07                          0.13 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                        136.6                         225.5 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                        27.16                         30.74 
[1] "0.1 - 136.6 (27.2)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.6"
D71V2, binary
                               cls
clus                              0   1
  DEL PEAK 21(9Q21.2) MUTATED    68  53
  DEL PEAK 21(9Q21.2) WILD-TYPE 222 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9Q21.2) MUTATED     68   53
  DEL PEAK 21(9Q21.2) WILD-TYPE  222  171
     clus
vv    DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE
  NO                           68                           222
  YES                          53                           171
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 21(9Q21.2) MUTATED                                        51
  DEL PEAK 21(9Q21.2) WILD-TYPE                                     353
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 21(9Q21.2) MUTATED                              10
  DEL PEAK 21(9Q21.2) WILD-TYPE                            12
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 21(9Q21.2) MUTATED                                  68
  DEL PEAK 21(9Q21.2) WILD-TYPE                                45
D71V3, multiclass
                                         clus
vv                                        DEL PEAK 21(9Q21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          51
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                68
                                         clus
vv                                        DEL PEAK 21(9Q21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           353
  MIXED SEROUS AND ENDOMETRIOID                                      12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(9Q21.2) MUTATED    80   5   7  13
  DEL PEAK 21(9Q21.2) WILD-TYPE 291  17   9  27
D71V4, multiclass
    clus
vv   DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE
  R0                          80                           291
  R1                           5                            17
  R2                           7                             9
  RX                          13                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = DEL PEAK 22(9Q34.2) MUTATION ANALYSIS
D72V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9Q34.2) MUTATED    92  39
  DEL PEAK 22(9Q34.2) WILD-TYPE 355  51
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          131                           406 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                           39                            51 
$`DEL PEAK 22(9Q34.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AX-A06B TCGA-AX-A1CP 
       41.06        20.81        10.19       110.63        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 
       23.05        61.18        27.88        80.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A221 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 
       66.41        12.56         1.81        16.93        33.30        10.19 
TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GR 
       14.40        23.74        39.52       123.68        65.75        36.82 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 
       37.91        17.59        42.35        31.99       118.19        28.64 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       25.51        20.25        21.14        34.16        18.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H 
        1.64        22.26        17.06        20.78        21.99        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX 
       36.89        48.79       125.42        97.71        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A3FS 
        0.56        37.78        34.65        76.83        30.12         0.23 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 
       43.82        20.52         0.30         0.26         0.39        27.29 
TCGA-B5-A0K8 TCGA-B5-A11H TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
       27.85        88.34        52.04       102.31        50.89        11.87 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A18C 
      136.60        39.35        29.65        34.13        34.95        15.45 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       35.08        31.00        24.13        61.87        92.88        83.64 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S 
        8.55        22.55        39.48        37.32        31.07        18.67 
TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G7 
        3.95        28.08        13.22         0.72         2.07        58.95 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN 
       18.84        17.29        71.61       109.08        25.91        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        9.37        31.10       110.10        79.10        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW 
       37.71        51.42        19.40        27.16        26.96        16.34 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW 
       54.15        23.90        32.71        17.62        15.81        11.08 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX 
       20.05        29.10        11.38        68.38        77.33         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       28.93        30.67        59.28        41.56        78.38        14.04 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
        9.47        26.10        18.21        23.24         4.44 

$`DEL PEAK 22(9Q34.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A3G3 TCGA-BG-A0MS 
       57.80        93.99        95.47        12.26         1.38        61.87 
TCGA-BG-A0VT TCGA-BG-A220 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 
       51.55        14.27        19.79         4.44        47.84         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 
       66.77        13.84        73.32        36.00         0.43        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37        74.10        60.53        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 
       29.06        15.95        31.99        36.33        33.07        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       24.72        34.95        14.96        11.21        18.41        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK 
       10.26        19.79        35.15        34.36        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       48.03        63.91        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        35.74        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       77.39        13.28        32.91        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       25.91        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.56         0.20         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW 
       18.41        17.36        16.57       225.50        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54        31.36        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       27.65        41.06        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       22.39        35.90        34.98        35.90        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83        29.95         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       23.93         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         0.69         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN 
        3.95        48.79         8.48        15.88         4.27         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        12.39        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       45.57        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        38.07        46.42        22.26        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       33.34        19.27        18.84        22.03        16.11        32.78 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       37.05        19.33        12.59        22.82        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 
       27.35        32.52        14.14        14.70        16.96        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-H5-A2HR TCGA-JU-AAVI 
        7.99        25.22        96.69        59.01         1.74        17.75 
TCGA-KP-A3W0 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       13.28        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                        136.6                         225.5 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                       28.640                        30.115 
[1] "0.2 - 136.6 (28.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.4"
D72V2, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.2) MUTATED    73  51
  DEL PEAK 22(9Q34.2) WILD-TYPE 217 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.2) MUTATED     73   51
  DEL PEAK 22(9Q34.2) WILD-TYPE  217  173
     clus
vv    DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE
  NO                           73                           217
  YES                          51                           173
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 22(9Q34.2) MUTATED                                        55
  DEL PEAK 22(9Q34.2) WILD-TYPE                                     349
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 22(9Q34.2) MUTATED                              10
  DEL PEAK 22(9Q34.2) WILD-TYPE                            12
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 22(9Q34.2) MUTATED                                  67
  DEL PEAK 22(9Q34.2) WILD-TYPE                                46
D72V3, multiclass
                                         clus
vv                                        DEL PEAK 22(9Q34.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          55
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                67
                                         clus
vv                                        DEL PEAK 22(9Q34.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           349
  MIXED SEROUS AND ENDOMETRIOID                                      12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9Q34.2) MUTATED    80   5   6  15
  DEL PEAK 22(9Q34.2) WILD-TYPE 291  17  10  25
D72V4, multiclass
    clus
vv   DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE
  R0                          80                           291
  R1                           5                            17
  R2                           6                            10
  RX                          15                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = DEL PEAK 23(10Q21.1) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10Q21.1) MUTATED    41   9
  DEL PEAK 23(10Q21.1) WILD-TYPE 406  81
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            50                            487 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                             9                             81 
$`DEL PEAK 23(10Q21.1) MUTATED`
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0KB 
       20.81        93.99        67.66        23.05         1.38        27.09 
TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       66.41        16.93        33.30        14.40        36.00        23.74 
TCGA-5B-A90C TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A3BF 
       39.52        31.99        36.33        14.96        18.41        18.12 
TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A3G1 TCGA-AX-A3G4 
       22.26        16.87        76.83         4.77        20.52         0.30 
TCGA-AX-A3GI TCGA-B5-A1MS TCGA-B5-A3FD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC 
        0.39       102.31        39.35        15.45        22.39        35.08 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A3DH TCGA-DI-A1NN 
       24.13        92.88        11.51        31.07        18.84        35.38 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GR TCGA-EY-A2OQ 
       51.42        27.16        22.26        16.34        17.62        29.10 
TCGA-EY-A3L3 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A914 
       27.35        77.33        96.69        78.38        14.04        22.59 
TCGA-PG-A915 TCGA-QS-A8F1 
        8.19         4.44 

$`DEL PEAK 23(10Q21.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D 
       18.08        10.19       110.63        57.80        95.47        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS 
       36.39        61.18        27.88        80.38        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 
       47.84         6.21        22.78        17.88        10.19        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
        0.43        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       54.02        23.21        68.65        37.91        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ 
       24.62        29.06        42.35        15.95        31.99        33.07 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
      118.19        66.15        28.64        24.72        34.95        25.51 
TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       11.21        20.25        14.43        10.26        21.14        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       35.15        34.36        34.16        18.90        33.90         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07        48.03        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37        66.25        36.36        97.71        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       32.02        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.26         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       31.36       136.60        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98        35.90        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU 
        4.27        17.29         2.20        71.61       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30         9.37        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       34.39        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        23.90        33.34        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       45.76        31.04        32.52        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       16.96        68.38        39.88         7.99        25.22        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
        9.34        28.93        30.67        59.28        41.56         1.74 
TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       17.75        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30        38.70        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                          0.30                           0.07 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        102.31                         225.50 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        23.395                         30.150 
[1] "0.3 - 102.3 (23.4)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.3"
D73V2, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    24  22
  DEL PEAK 23(10Q21.1) WILD-TYPE 266 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     24   22
  DEL PEAK 23(10Q21.1) WILD-TYPE  266  202
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  NO                            24                            266
  YES                           22                            202
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                                        16
  DEL PEAK 23(10Q21.1) WILD-TYPE                                     388
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 23(10Q21.1) MUTATED                               4
  DEL PEAK 23(10Q21.1) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                                  30
  DEL PEAK 23(10Q21.1) WILD-TYPE                                83
D73V3, multiclass
                                         clus
vv                                        DEL PEAK 23(10Q21.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           16
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 30
                                         clus
vv                                        DEL PEAK 23(10Q21.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            388
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10Q21.1) MUTATED    32   1   2   6
  DEL PEAK 23(10Q21.1) WILD-TYPE 339  21  14  34
D73V4, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  R0                           32                            339
  R1                            1                             21
  R2                            2                             14
  RX                            6                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = DEL PEAK 24(10Q23.31) MUTATION ANALYSIS
D74V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED    54  23
  DEL PEAK 24(10Q23.31) WILD-TYPE 393  67
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             77                             460 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             23                              67 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CR 
       41.06        29.39        20.81        93.99        67.66        23.05 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-EY-A214 
        1.38        80.38        27.09        66.41        16.93        14.40 
TCGA-KJ-A3U4 TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LP 
       36.00       123.68        65.75        31.99        36.33        14.96 
TCGA-A5-A7WK TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A0L9 
       18.41        18.12        22.26        16.87        21.99       125.42 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
       36.13         0.56         2.96        20.52         0.30         0.26 
TCGA-AX-A3GI TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A1MS TCGA-B5-A3FD TCGA-BG-A18C 
        0.39        72.62        27.29       102.31        39.35        15.45 
TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-D1-A160 TCGA-D1-A16I 
       22.39        24.13         4.80        92.88         3.68        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 
       29.92        31.07        28.01        28.08        13.22         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DI-A1NN TCGA-DI-A2QY TCGA-EO-A1Y5 
        4.27        18.84        71.61        35.38       110.10        10.92 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW 
       51.42        19.40        34.39        27.16        26.96        16.34 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A3L3 
       23.90        32.71        17.62        22.03        11.08        27.35 
TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI 
       11.38        77.33        96.69        30.67        41.56        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A914 TCGA-QS-A8F1 
       14.04        26.10        18.21        22.59         4.44 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3NH 
       88.18        60.53        30.15        16.83        18.08        10.19 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
      110.63        57.80        95.47        12.26        36.39        61.18 
TCGA-AX-A2HF TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       27.88        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 
       22.78        17.88        10.19        18.87        17.92        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KP-A3VZ TCGA-4E-A92E 
        5.88        66.77        13.84        73.32        23.74         0.43 
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       39.52        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GN 
       17.85        32.78       112.54       105.37        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        37.91        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       42.35        15.95        31.99        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23M 
       28.64        24.72        34.95        25.51        11.21        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       48.03        63.91        45.53        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91        48.79       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S 
       60.23        45.86        27.85        51.12        21.90        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       77.39        13.28        32.91        34.65        25.51        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       71.44        48.59        36.49        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
       75.72        54.44        73.64        61.68        85.78        52.04 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        48.43        11.87        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        93.50        71.84        27.65        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
       24.99        16.64        13.18        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       24.33        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 
       21.99        39.48        30.08        29.88         1.91        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        27.42        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       30.44         1.28        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JQ TCGA-DF-A2KN 
       48.79         8.48        58.95        15.88        17.29         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT 
       16.31        39.29        36.62        24.30         9.37        12.39 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        51.52        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        38.07        46.42        22.26        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        19.27        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A 
       45.76        31.04        29.10        32.52        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       16.96        68.38        39.88         7.99        25.22        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W0 
        9.34        28.93        59.28        78.38         1.74        13.28 
TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 
        9.47        23.24        21.30        38.70         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.26                            0.07 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         125.42                          225.50 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                          23.90                           31.07 
[1] "0.3 - 125.4 (23.9)" "0.1 - 225.5 (31.1)"
[1] "hr=" "2.4"
D74V2, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    41  31
  DEL PEAK 24(10Q23.31) WILD-TYPE 249 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     41   31
  DEL PEAK 24(10Q23.31) WILD-TYPE  249  193
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                             41                             249
  YES                            31                             193
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                                        32
  DEL PEAK 24(10Q23.31) WILD-TYPE                                     372
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 24(10Q23.31) MUTATED                               6
  DEL PEAK 24(10Q23.31) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                                  40
  DEL PEAK 24(10Q23.31) WILD-TYPE                                73
D74V3, multiclass
                                         clus
vv                                        DEL PEAK 24(10Q23.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            32
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  40
                                         clus
vv                                        DEL PEAK 24(10Q23.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             372
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 24(10Q23.31) MUTATED    48   2   5   8
  DEL PEAK 24(10Q23.31) WILD-TYPE 323  20  11  32
D74V4, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  R0                            48                             323
  R1                             2                              20
  R2                             5                              11
  RX                             8                              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = DEL PEAK 25(11P15.5) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(11P15.5) MUTATED    74  29
  DEL PEAK 25(11P15.5) WILD-TYPE 373  61
  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                           103                            434 
  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                            29                             61 
$`DEL PEAK 25(11P15.5) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-B5-A0JN 
       41.06        20.81        10.19        93.99        23.05        80.38 
TCGA-B5-A0KB TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A214 TCGA-KJ-A3U4 
       27.09        12.56        16.93        33.30        14.40        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG 
       23.74        39.52       149.56        65.75        60.53        31.99 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A7WK TCGA-AJ-A23M 
       36.33       118.19        66.15        28.64        18.41        20.25 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       21.14        34.16        18.12        18.90         1.64        22.26 
TCGA-AJ-A3NF TCGA-AP-A05A TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IW 
       21.21        63.91        97.71        46.78        21.90        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A3FW 
       34.65        32.02        76.83         4.77        30.12         0.56 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11P 
       20.52         0.30         0.26         0.39        27.85        52.04 
TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE 
      102.31        31.36       136.60        39.35        34.13        34.95 
TCGA-BG-A0MC TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-D1-A15V 
       41.52        35.08        31.00        16.64        61.87        39.48 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1NX 
       37.32        11.51        18.67        28.08         0.72        18.25 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 
        2.07         4.27        18.84        71.61       109.08        25.91 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y8 
        9.37        12.39        31.10       110.10        79.10        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EY-A1GJ TCGA-EY-A1GO 
       51.42        19.40        34.39        26.96        23.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A54A 
       18.84        17.62        22.03        45.76        29.10        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR 
       77.33        59.01         9.34        28.93        41.56         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       17.75        14.04         9.47        23.24        38.70         8.19 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 25(11P15.5) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        95.47        67.66        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       61.18        27.88         1.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       51.55        14.27         1.81        19.79         4.44        47.84 
TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 
        6.21        22.78        17.88        10.19        18.87        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       19.89         5.88        66.77        13.84        73.32         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37       123.68        74.10        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       31.99        33.07        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       11.21        14.43        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       33.90        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
      129.80        21.99        23.31        86.07        48.03        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       26.37        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.23         0.20        43.82         0.20         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      225.50        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       52.54        96.30        93.50        71.84        27.65        29.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MI 
       71.24        63.68        74.63        10.72        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       14.83        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31        22.39 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98        35.90        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU 
        8.48        58.95        15.88        17.29         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        35.38        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        51.52        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GT 
       27.16        23.34        23.34        33.34        32.71        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       32.78        15.81        11.08        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       22.82        20.05        31.04        27.35        32.52        11.38 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KP-A3W0 TCGA-KP-A3W3 
       96.69        30.67        59.28        78.38        13.28        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        21.30        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                        149.56                         225.50 
  DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE 
                        28.080                         30.115 
[1] "0.1 - 149.6 (28.1)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.1"
D75V2, binary
                                cls
clus                               0   1
  DEL PEAK 25(11P15.5) MUTATED    54  39
  DEL PEAK 25(11P15.5) WILD-TYPE 236 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(11P15.5) MUTATED     54   39
  DEL PEAK 25(11P15.5) WILD-TYPE  236  185
     clus
vv    DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE
  NO                            54                            236
  YES                           39                            185
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 25(11P15.5) MUTATED                                        40
  DEL PEAK 25(11P15.5) WILD-TYPE                                     364
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 25(11P15.5) MUTATED                               6
  DEL PEAK 25(11P15.5) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 25(11P15.5) MUTATED                                  58
  DEL PEAK 25(11P15.5) WILD-TYPE                                55
D75V3, multiclass
                                         clus
vv                                        DEL PEAK 25(11P15.5) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           40
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 58
                                         clus
vv                                        DEL PEAK 25(11P15.5) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            364
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(11P15.5) MUTATED    63   3   7  11
  DEL PEAK 25(11P15.5) WILD-TYPE 308  19   9  29
D75V4, multiclass
    clus
vv   DEL PEAK 25(11P15.5) MUTATED DEL PEAK 25(11P15.5) WILD-TYPE
  R0                           63                            308
  R1                            3                             19
  R2                            7                              9
  RX                           11                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = DEL PEAK 26(11Q14.1) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11Q14.1) MUTATED    51  18
  DEL PEAK 26(11Q14.1) WILD-TYPE 396  72
  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                            69                            468 
  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                            18                             72 
$`DEL PEAK 26(11Q14.1) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AX-A1CR TCGA-BG-A0M6 TCGA-BG-A0YV 
       29.39        10.19        93.99        23.05        22.06        12.56 
TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       16.93        33.30         5.88        36.00        23.74        39.52 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K3 
       60.53        36.82        37.91        31.99       118.19        66.15 
TCGA-A5-A2K4 TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3QS 
       28.64        21.14        34.16        18.90         1.64        16.87 
TCGA-AJ-A3TW TCGA-AP-A3K1 TCGA-AX-A1C7 TCGA-AX-A2IO TCGA-AX-A3G6 TCGA-B5-A0K3 
       16.87        21.90        34.65        64.93         0.26        27.29 
TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD 
       27.85        52.04        32.09       136.60        39.35        34.13 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
       22.39        35.08        24.13        22.55        37.32        11.51 
TCGA-D1-A16S TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EO-A1Y8 
       18.67         4.27        35.38         9.37        12.39        37.71 
TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       51.42        22.26        23.90        19.27        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR 
       22.03        11.08        12.59        45.76        27.35        11.38 
TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-JU-AAVI 
       14.70        77.33        96.69         9.34        28.93        17.75 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A915 
        9.47        26.10         8.19 

$`DEL PEAK 26(11Q14.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       20.81       110.63        57.80        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB 
       36.39        61.18        27.88         1.38        80.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 
        4.44        47.84         6.21        22.78        17.88        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       14.40        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       73.32         0.43        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        65.75        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K5 
       42.35        15.95        31.99        36.33        33.07        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M 
       34.95        25.51        14.96        11.21        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       14.43        10.26        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       33.90        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.62        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      125.42       117.99       110.37        66.25        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       45.86        27.85        51.12        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.21        29.69        80.55        88.24        71.51        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        79.46        49.87        57.47        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        61.08        35.74        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       77.39        13.28        32.91        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.58         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        38.24        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.30         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       85.78        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       225.50       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        93.50        71.84        27.65        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       16.64        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN 
        8.48        58.95        15.88        18.84        17.29         2.20 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       71.61       109.08       100.83        89.33        10.92        27.16 
TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU 
       25.91        16.31        39.29        36.62        24.30        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       26.96        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GM TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       32.71        16.11        32.78        15.81        37.05        19.33 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 
       22.82        20.05        31.04        29.10        32.52        14.14 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       16.96        68.38        39.88         7.99        25.22        59.01 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       30.67        59.28        41.56        78.38         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       13.28        18.21        23.24        21.30        38.70        22.59 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.07         0.23 

  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                          0.26                           0.07 
  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE 
                        23.900                         30.705 
[1] "0.3 - 136.6 (23.9)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2"  
D76V2, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q14.1) MUTATED    34  32
  DEL PEAK 26(11Q14.1) WILD-TYPE 256 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q14.1) MUTATED     34   32
  DEL PEAK 26(11Q14.1) WILD-TYPE  256  192
     clus
vv    DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE
  NO                            34                            256
  YES                           32                            192
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 26(11Q14.1) MUTATED                                        21
  DEL PEAK 26(11Q14.1) WILD-TYPE                                     383
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 26(11Q14.1) MUTATED                               6
  DEL PEAK 26(11Q14.1) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 26(11Q14.1) MUTATED                                  42
  DEL PEAK 26(11Q14.1) WILD-TYPE                                71
D76V3, multiclass
                                         clus
vv                                        DEL PEAK 26(11Q14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           21
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 42
                                         clus
vv                                        DEL PEAK 26(11Q14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            383
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(11Q14.1) MUTATED    46   4   3   6
  DEL PEAK 26(11Q14.1) WILD-TYPE 325  18  13  34
D76V4, multiclass
    clus
vv   DEL PEAK 26(11Q14.1) MUTATED DEL PEAK 26(11Q14.1) WILD-TYPE
  R0                           46                            325
  R1                            4                             18
  R2                            3                             13
  RX                            6                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = DEL PEAK 27(11Q25) MUTATION ANALYSIS
D77V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 27(11Q25) MUTATED    68  26
  DEL PEAK 27(11Q25) WILD-TYPE 379  64
  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                          94                          443 
  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                          26                           64 
$`DEL PEAK 27(11Q25) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-BG-A0M6 
       29.39        20.81        10.19        57.80        93.99        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A214 TCGA-FI-A2CX TCGA-KJ-A3U4 
       66.41        12.56        16.93        14.40        66.77        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 
       23.74        39.52        65.75        60.53        36.82        17.59 
TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A3BD TCGA-AJ-A3BI 
       31.99       118.19        66.15        28.64        34.16        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A3K1 TCGA-AP-A5FX 
        1.64        16.87        16.87        21.99        21.90        36.13 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       34.65        25.51        64.93         0.30         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MU 
        0.39        27.29        27.85        52.04        32.09        50.89 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0MC TCGA-BG-A18C 
       31.36       136.60        39.35        34.13        41.52        15.45 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A169 
       22.39        35.08        24.13        16.64        22.55        37.32 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A3DG TCGA-DF-A2KS TCGA-DI-A1NN 
       11.51        18.67         3.95         4.27       109.08        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        9.37        12.39        31.10        10.92        49.15        37.71 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM 
       57.60        51.42        22.26        16.34        23.90        32.71 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 
       19.27        18.84        17.62        22.03        11.08        12.59 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A 
       20.05        45.76        27.35        32.52        11.38        14.70 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI 
       96.69         9.34        28.93        30.67         1.74        17.75 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A914 TCGA-PG-A915 
        9.47        26.10        22.59         8.19 

$`DEL PEAK 27(11Q25) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR 
      110.63        95.47        67.66        12.26        36.39        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0MS 
       61.18        27.88         1.38        80.38        27.09        61.87 
TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       51.55        14.27         1.81        19.79         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 
       33.30         6.21        22.78        17.88        10.19        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       17.92        19.89         5.88        13.84        73.32         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP 
       32.78       112.54       105.37       123.68        74.10        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       73.87        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       36.33        33.07        24.72        34.95        25.51        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
       11.21        18.41        20.25        14.43        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK 
       19.79        35.15        34.36        18.12        33.90        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        77.39        13.28        32.91        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.02        25.91        34.09        76.83        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       80.25        37.58         4.77        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
        2.96        31.13         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20        20.52         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R 
       75.72        54.44        73.64        61.68        85.78        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       225.50       102.31        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       11.87        52.54        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU 
       15.88        18.84        17.29         2.20        71.61       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       36.62        24.30       110.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R 
        2.37        45.57        16.04         7.36        16.80        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       61.55        66.90        46.26        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GT TCGA-EY-A1GU 
       27.16        23.34        23.34        33.34        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ 
       15.81        37.05        19.33        22.82        31.04        29.10 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.14        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       25.22        59.01        59.28        41.56        78.38        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 
       13.28        18.21        23.24        21.30        38.70        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                        0.26                         0.07 
  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                       136.6                        225.5 
  DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE 
                      24.015                       30.740 
[1] "0.3 - 136.6 (24.0)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.3"
D77V2, binary
                              cls
clus                             0   1
  DEL PEAK 27(11Q25) MUTATED    49  37
  DEL PEAK 27(11Q25) WILD-TYPE 241 187
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 27(11Q25) MUTATED     49   37
  DEL PEAK 27(11Q25) WILD-TYPE  241  187
     clus
vv    DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE
  NO                          49                          241
  YES                         37                          187
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 27(11Q25) MUTATED                                        33
  DEL PEAK 27(11Q25) WILD-TYPE                                     371
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 27(11Q25) MUTATED                               6
  DEL PEAK 27(11Q25) WILD-TYPE                            16
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 27(11Q25) MUTATED                                  55
  DEL PEAK 27(11Q25) WILD-TYPE                                58
D77V3, multiclass
                                         clus
vv                                        DEL PEAK 27(11Q25) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         33
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               55
                                         clus
vv                                        DEL PEAK 27(11Q25) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          371
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 27(11Q25) MUTATED    60   4   5  10
  DEL PEAK 27(11Q25) WILD-TYPE 311  18  11  30
D77V4, multiclass
    clus
vv   DEL PEAK 27(11Q25) MUTATED DEL PEAK 27(11Q25) WILD-TYPE
  R0                         60                          311
  R1                          4                           18
  R2                          5                           11
  RX                         10                           30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = DEL PEAK 28(12Q23.1) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(12Q23.1) MUTATED    37  19
  DEL PEAK 28(12Q23.1) WILD-TYPE 410  71
  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                            56                            481 
  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                            19                             71 
$`DEL PEAK 28(12Q23.1) MUTATED`
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-B5-A0JN TCGA-BG-A0YV TCGA-D1-A3JP 
       20.81        10.19        93.99        80.38        12.56        16.93 
TCGA-EY-A212 TCGA-EY-A214 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0R6 
       10.19        14.40        23.74        39.52        65.75        37.91 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A3NF TCGA-AP-A052 TCGA-AP-A05H 
       36.33       118.19        28.64        21.21        21.99        45.53 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A2H2 
       97.71        33.40        21.90        36.13         0.56         4.77 
TCGA-B5-A0K3 TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BK-A139 
       27.29        31.36        34.13        34.95        15.45        31.00 
TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A3DH TCGA-D1-A3JQ 
       24.13        22.55        39.48        18.67        18.84        17.29 
TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A3AZ 
       71.61        25.91        12.39       110.10        10.92        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU 
       26.96        16.34        29.10        11.38        14.70        96.69 
TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
       41.56        17.75        14.04        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A915 
       23.24         8.19 

$`DEL PEAK 28(12Q23.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM 
       41.06        88.18        60.53        30.15        16.83        29.39 
TCGA-AJ-A3BG TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       18.08       110.63        57.80        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB 
       36.39        23.05        61.18        27.88         1.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
       22.06        66.41        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       17.88        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        60.53        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       36.82        28.27        54.02        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       31.99        33.07        66.15        24.72        34.95        25.51 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       14.96        11.21        18.41        20.25        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       21.14        19.79        35.15        34.36        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       48.03        63.91        36.89        23.87        12.62        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       46.72        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.85        51.12        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 
       76.83        85.48        73.41        80.25        37.58        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.20         0.56        43.82         0.20        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      113.36        88.34        75.72        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       52.54       136.60        96.30        93.50        71.84        39.35 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       27.65        29.65        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       61.87        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
       23.93         1.74        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        4.27         2.20       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        31.10        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       45.57        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       46.42        22.26        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       33.34        32.71        19.27        18.84        17.62        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        32.78        15.81        11.08        37.05        19.33 
TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       32.52        14.14        16.96        68.38        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
        7.99        25.22        59.01         9.34        28.93        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A7D5 
       59.28        78.38         1.74         9.47        21.30        38.70 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       22.59        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                          0.56                           0.07 
  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                        118.19                         225.50 
  DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE 
                        23.935                         30.670 
[1] "0.6 - 118.2 (23.9)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.7"
D78V2, binary
                                cls
clus                               0   1
  DEL PEAK 28(12Q23.1) MUTATED    26  27
  DEL PEAK 28(12Q23.1) WILD-TYPE 264 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(12Q23.1) MUTATED     26   27
  DEL PEAK 28(12Q23.1) WILD-TYPE  264  197
     clus
vv    DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE
  NO                            26                            264
  YES                           27                            197
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 28(12Q23.1) MUTATED                                        14
  DEL PEAK 28(12Q23.1) WILD-TYPE                                     390
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 28(12Q23.1) MUTATED                               3
  DEL PEAK 28(12Q23.1) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 28(12Q23.1) MUTATED                                  39
  DEL PEAK 28(12Q23.1) WILD-TYPE                                74
D78V3, multiclass
                                         clus
vv                                        DEL PEAK 28(12Q23.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           14
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 39
                                         clus
vv                                        DEL PEAK 28(12Q23.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            390
  MIXED SEROUS AND ENDOMETRIOID                                       19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(12Q23.1) MUTATED    34   1   4   9
  DEL PEAK 28(12Q23.1) WILD-TYPE 337  21  12  31
D78V4, multiclass
    clus
vv   DEL PEAK 28(12Q23.1) MUTATED DEL PEAK 28(12Q23.1) WILD-TYPE
  R0                           34                            337
  R1                            1                             21
  R2                            4                             12
  RX                            9                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = DEL PEAK 29(12Q24.33) MUTATION ANALYSIS
D79V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(12Q24.33) MUTATED    48  18
  DEL PEAK 29(12Q24.33) WILD-TYPE 399  72
  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                             66                             471 
  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                             18                              72 
$`DEL PEAK 29(12Q24.33) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0YV 
       29.39        20.81        10.19         1.38        80.38        12.56 
TCGA-EY-A214 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A1OG TCGA-A5-A1OH 
       14.40         5.88        23.74        39.52        31.99        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BI TCGA-AJ-A3NF 
      118.19        28.64        14.96        14.43        18.90        21.21 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO 
       21.99        45.53        97.71        33.40        21.90         0.56 
TCGA-AX-A1C7 TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-B5-A0K8 
       34.65        25.91        76.83         4.77        71.24        27.85 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L TCGA-D1-A0ZZ 
       29.65        34.95        15.45        31.00        24.13        22.55 
TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JQ 
       39.48        18.67        28.08         2.07        18.84        17.29 
TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
      109.08        25.91        12.39        31.10       110.10        79.10 
TCGA-EO-A1Y5 TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A2OQ 
       10.92        34.39        27.16        16.34        54.15        29.10 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ 
       11.38        14.70        96.69        41.56        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A915 TCGA-SL-A6J9 
       13.28        26.10        18.21        38.70         8.19         0.07 

$`DEL PEAK 29(12Q24.33) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
      110.63        57.80        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M6 
       36.39        23.05        61.18        27.88        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX 
       17.88        10.19        18.87        17.92        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32        36.00         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GP 
      105.37       123.68        74.10        65.75        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       37.91        17.59        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       15.95        31.99        33.07        66.15        24.72        34.95 
TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
       25.51        11.21        18.41        20.25        10.26        21.14 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.12        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.64        14.66        22.49        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13       129.80        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       26.37        32.02        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        30.12        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       38.24        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       27.29        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        73.64 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       61.68        85.78        52.04        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       71.84        39.35        27.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
       35.90        35.08        31.76        24.99        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        92.88       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        28.67        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
       13.22         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
        4.27         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
        9.37        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       50.73        35.15        38.07        46.42        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 
       45.76        31.04        27.35        32.52        14.14        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW 
       68.38        39.88        77.33         7.99        25.22        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
        9.34        28.93        30.67        59.28        78.38         1.74 
TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
        9.47        23.24        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       22.65        39.95        24.95        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                           0.07                            0.13 
  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                         118.19                          225.50 
  DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE 
                          25.02                           30.74 
[1] "0.1 - 118.2 (25.0)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.1"
D79V2, binary
                                 cls
clus                                0   1
  DEL PEAK 29(12Q24.33) MUTATED    31  29
  DEL PEAK 29(12Q24.33) WILD-TYPE 259 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(12Q24.33) MUTATED     31   29
  DEL PEAK 29(12Q24.33) WILD-TYPE  259  195
     clus
vv    DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE
  NO                             31                             259
  YES                            29                             195
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 29(12Q24.33) MUTATED                                        20
  DEL PEAK 29(12Q24.33) WILD-TYPE                                     384
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 29(12Q24.33) MUTATED                               2
  DEL PEAK 29(12Q24.33) WILD-TYPE                            20
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 29(12Q24.33) MUTATED                                  44
  DEL PEAK 29(12Q24.33) WILD-TYPE                                69
D79V3, multiclass
                                         clus
vv                                        DEL PEAK 29(12Q24.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            20
  MIXED SEROUS AND ENDOMETRIOID                                       2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  44
                                         clus
vv                                        DEL PEAK 29(12Q24.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             384
  MIXED SEROUS AND ENDOMETRIOID                                        20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 29(12Q24.33) MUTATED    40   2   5  10
  DEL PEAK 29(12Q24.33) WILD-TYPE 331  20  11  30
D79V4, multiclass
    clus
vv   DEL PEAK 29(12Q24.33) MUTATED DEL PEAK 29(12Q24.33) WILD-TYPE
  R0                            40                             331
  R1                             2                              20
  R2                             5                              11
  RX                            10                              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = DEL PEAK 30(13Q11) MUTATION ANALYSIS
D80V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 30(13Q11) MUTATED    70  27
  DEL PEAK 30(13Q11) WILD-TYPE 377  63
  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                          97                          440 
  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                          27                           63 
$`DEL PEAK 30(13Q11) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A2HF 
       41.06        29.39        10.19        67.66        36.39        27.88 
TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A547 
        1.38        27.09        22.06        12.56        16.93        17.92 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 
       36.00        23.74       149.56        65.75        60.53        17.59 
TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       42.35        36.33       118.19        28.64        25.51        14.96 
TCGA-A5-A7WK TCGA-AJ-A2QK TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
       18.41        21.14        18.90         1.64        22.26        17.06 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0L8 
       16.87        16.87        20.78        45.53        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AX-A1C7 TCGA-AX-A1C9 
      125.42        97.71        33.40        36.13        34.65        26.37 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G1 
       32.02        76.83        30.12         2.96        64.93        20.52 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
        0.30         0.39        52.04        50.89        11.87        31.36 
TCGA-B5-A3F9 TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD 
      136.60        34.95        15.45        22.39        31.00        16.64 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A1NU 
       61.87        92.88        37.32        31.07        14.73        13.22 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO 
        4.27        17.29       109.08        25.91        35.38         9.37 
TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GP 
      110.10        10.92        49.15        51.42        27.16        18.84 
TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ 
       17.62        15.81        11.08        20.05        45.76        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       32.52        11.38         7.99        30.67        41.56        78.38 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       13.28        26.10        18.21        23.24        38.70        22.59 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 30(13Q11) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CR 
      110.63        57.80        93.99        95.47        12.26        23.05 
TCGA-AX-A2H8 TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 
       61.18        80.38        66.41        61.87        51.55        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        33.30         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
       22.78        17.88        10.19        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C 
        5.88        66.77        13.84        73.32         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37       123.68        74.10        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       19.59        24.62        29.06        15.95        31.99        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23M 
       33.07        66.15        24.72        34.95        11.21        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       14.43        10.26        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE 
       18.12        33.90        14.66        22.49        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       12.62       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       83.97        27.12        82.52        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        21.90         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.74        37.78        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       32.91        25.51        25.91        34.09        85.48        73.41 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       80.25        37.58         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        38.24        17.75        30.74        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 
        0.23         0.20         0.56        43.82         0.20         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50       102.31        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        48.43        52.54        96.30        93.50        71.84 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       39.35        27.65        29.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       35.08        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       77.95        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       36.10        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KN 
       48.79         8.48        58.95        15.88        18.84         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
       71.61       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       79.10        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       38.07        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       22.03        16.11        32.78        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       22.82        31.04        27.35        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       68.38        39.88        77.33        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
        9.34        28.93        59.28         1.74        17.75        14.04 
TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.47        21.30         8.19        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                        0.07                         0.13 
  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                      149.56                       225.50 
  DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE 
                       26.37                        30.59 
[1] "0.1 - 149.6 (26.4)" "0.1 - 225.5 (30.6)"
[1] "hr=" "2.1"
D80V2, binary
                              cls
clus                             0   1
  DEL PEAK 30(13Q11) MUTATED    52  39
  DEL PEAK 30(13Q11) WILD-TYPE 238 185
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 30(13Q11) MUTATED     52   39
  DEL PEAK 30(13Q11) WILD-TYPE  238  185
     clus
vv    DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE
  NO                          52                          238
  YES                         39                          185
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 30(13Q11) MUTATED                                        41
  DEL PEAK 30(13Q11) WILD-TYPE                                     363
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 30(13Q11) MUTATED                               6
  DEL PEAK 30(13Q11) WILD-TYPE                            16
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 30(13Q11) MUTATED                                  51
  DEL PEAK 30(13Q11) WILD-TYPE                                62
D80V3, multiclass
                                         clus
vv                                        DEL PEAK 30(13Q11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         41
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               51
                                         clus
vv                                        DEL PEAK 30(13Q11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          363
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 30(13Q11) MUTATED    64   5   5  10
  DEL PEAK 30(13Q11) WILD-TYPE 307  17  11  30
D80V4, multiclass
    clus
vv   DEL PEAK 30(13Q11) MUTATED DEL PEAK 30(13Q11) WILD-TYPE
  R0                         64                          307
  R1                          5                           17
  R2                          5                           11
  RX                         10                           30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(81) Variable = DEL PEAK 31(13Q14.2) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(13Q14.2) MUTATED    76  29
  DEL PEAK 31(13Q14.2) WILD-TYPE 371  61
  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                           105                            432 
  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                            29                             61 
$`DEL PEAK 31(13Q14.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A3G3 
       41.06        29.39        10.19        67.66        36.39         1.38 
TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A547 
       27.09        22.06        12.56        16.93        33.30        17.92 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN 
       36.00        23.74        10.29       149.56        65.75        60.53 
TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP 
       17.59        42.35        36.33       118.19        25.51        14.96 
TCGA-A5-A7WK TCGA-AJ-A2QK TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
       18.41        21.14        18.90         1.64        22.26        17.06 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0LI 
       16.87        16.87        20.78        45.53        20.91        97.71 
TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A1C9 TCGA-AX-A1CF TCGA-AX-A1CK 
       33.40        36.13         0.56        26.37        76.83        80.25 
TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       30.12         2.96         0.56        43.82        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY 
        0.26         0.39        27.29        52.04        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE 
       31.36       136.60        39.35        34.95        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A169 
       22.39        31.00        16.64        61.87        92.88        37.32 
TCGA-D1-A16N TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A3DG 
       31.07         3.95        14.73        28.08        13.22         4.27 
TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-EO-A1Y7 
       71.61       109.08        25.91        35.38         9.37        49.15 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV 
       34.39        27.16        54.15        18.84        17.62        15.81 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX 
       11.08        12.59        20.05        45.76        29.10        32.52 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-SL-A6J9 
       23.24        38.70         0.07 

$`DEL PEAK 31(13Q14.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CR 
      110.63        57.80        93.99        95.47        12.26        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       61.18        27.88        80.38        66.41        61.87        51.55 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 
       14.27         1.81        19.79         4.44        47.84         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 
       22.78        17.88        10.19        14.40        18.87        19.89 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C 
        5.88        66.77        13.84        73.32         0.43        39.52 
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      106.88        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      105.37       123.68        74.10        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        37.91        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       24.62        29.06        15.95        31.99        31.99        33.07 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23M 
       66.15        28.64        24.72        34.95        11.21        20.25 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       14.43        10.26        19.79        35.15        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE 
       18.12        33.90        14.66        22.49        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        48.79       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        46.72        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T 
       45.86        27.85        51.12        21.90        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       61.08        35.74        37.78        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        32.91        34.65        25.51        32.02        25.91 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       34.09        85.48        73.41        37.58         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        81.37        34.32        46.49        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       30.74        31.13        64.93         0.23         0.20         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       48.59        36.49        72.62        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       27.85        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       225.50       102.31        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       48.43        52.54        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.01        15.45         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        35.08        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 
       72.72        73.25        59.51        89.59        63.58        83.64 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       86.99        66.48        16.83        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        4.87        28.67        23.93        22.55         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69        18.67         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH 
        3.95        48.79         8.48        58.95        15.88        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       17.29         2.20       100.83        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       19.40        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       22.26        16.34        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       32.71        19.27        22.03        16.11        32.78        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 
       19.33        22.82        31.04        27.35        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        68.38        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-H5-A2HR TCGA-PG-A6IB TCGA-PG-A914 
       25.22        96.69        59.01         1.74        21.30        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        20.75        18.28         0.23 

  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                        149.56                         225.50 
  DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE 
                         25.91                          31.07 
[1] "0.1 - 149.6 (25.9)" "0.1 - 225.5 (31.1)"
[1] "hr=" "2.3"
D81V2, binary
                                cls
clus                               0   1
  DEL PEAK 31(13Q14.2) MUTATED    60  37
  DEL PEAK 31(13Q14.2) WILD-TYPE 230 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(13Q14.2) MUTATED     60   37
  DEL PEAK 31(13Q14.2) WILD-TYPE  230  187
     clus
vv    DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE
  NO                            60                            230
  YES                           37                            187
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 31(13Q14.2) MUTATED                                        54
  DEL PEAK 31(13Q14.2) WILD-TYPE                                     350
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 31(13Q14.2) MUTATED                               7
  DEL PEAK 31(13Q14.2) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 31(13Q14.2) MUTATED                                  45
  DEL PEAK 31(13Q14.2) WILD-TYPE                                68
D81V3, multiclass
                                         clus
vv                                        DEL PEAK 31(13Q14.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           54
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 45
                                         clus
vv                                        DEL PEAK 31(13Q14.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            350
  MIXED SEROUS AND ENDOMETRIOID                                       15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(13Q14.2) MUTATED    69   2   4   9
  DEL PEAK 31(13Q14.2) WILD-TYPE 302  20  12  31
D81V4, multiclass
    clus
vv   DEL PEAK 31(13Q14.2) MUTATED DEL PEAK 31(13Q14.2) WILD-TYPE
  R0                           69                            302
  R1                            2                             20
  R2                            4                             12
  RX                            9                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(82) Variable = DEL PEAK 32(14Q13.1) MUTATION ANALYSIS
D82V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(14Q13.1) MUTATED    54  19
  DEL PEAK 32(14Q13.1) WILD-TYPE 393  71
  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                            73                            464 
  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                            19                             71 
$`DEL PEAK 32(14Q13.1) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AX-A1CR TCGA-B5-A0JN TCGA-B5-A0KB TCGA-D1-A3JP 
       29.39        10.19        23.05        80.38        27.09        16.93 
TCGA-E6-A8L9 TCGA-EY-A214 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A2K4 
       33.30        14.40        60.53        37.91        17.59        28.64 
TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EL TCGA-AJ-A6NU 
       20.25        34.16        18.90         1.64        22.49        20.78 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LO TCGA-AP-A1E0 TCGA-AX-A0IW 
       45.53        48.79       125.42        33.40        60.23        37.78 
TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G6 
       32.02         4.77         2.96         0.56        20.52         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 
        0.30         0.39        27.85        52.04        11.87        31.36 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD 
       29.65        34.13        15.45        35.08        31.00        16.64 
TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A3JQ TCGA-DF-A2KS 
       11.51        14.73        13.22         0.72        17.29       109.08 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW 
       35.38        12.39        51.42        34.39        22.26        16.34 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2OO TCGA-EY-A2OQ 
       23.90        19.27        17.62        22.03        45.76        29.10 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 
       11.38        14.70        68.38        96.69        30.67        59.28 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       78.38         1.74        17.75        38.70         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 32(14Q13.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B 
       20.81       110.63        57.80        93.99        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 
       12.26        36.39        61.18        27.88         1.38        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       66.41        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
       19.79         4.44        47.84         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       10.19        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C 
       13.84        73.32        36.00        23.74         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ 
       32.78       112.54       105.37       123.68        74.10        65.75 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       24.72        34.95        25.51        14.96        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       18.12        33.90        14.66        22.26        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        16.87        22.32        12.82         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13       129.80        21.99        23.31        86.07        48.03 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       63.91        36.89        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       27.12        82.52        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
       49.15         6.71        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        77.39        13.28        32.91        34.65 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       25.51        26.37        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       73.41        80.25        37.58        30.12        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20        43.82         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       75.72        54.44        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       225.50       102.31        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       71.84        39.35        27.65        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       35.90        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV 
        4.27        18.84         2.20        71.61       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       10.92        27.16        25.91        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       24.30         9.37        31.10       110.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.52        19.40        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 
       38.07        27.16        46.42        26.96        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99        54.15        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        32.71        18.84        16.11        32.78 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       15.81        11.08        37.05        19.33        12.59        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 
       20.05        31.04        27.35        32.52        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88        77.33         7.99        25.22        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       28.93        41.56        14.04        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       18.21        23.24        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                        125.42                         225.50 
  DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE 
                         22.49                          30.74 
[1] "0.1 - 125.4 (22.5)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.2"
D82V2, binary
                                cls
clus                               0   1
  DEL PEAK 32(14Q13.1) MUTATED    37  29
  DEL PEAK 32(14Q13.1) WILD-TYPE 253 195
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(14Q13.1) MUTATED     37   29
  DEL PEAK 32(14Q13.1) WILD-TYPE  253  195
     clus
vv    DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE
  NO                            37                            253
  YES                           29                            195
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 32(14Q13.1) MUTATED                                        26
  DEL PEAK 32(14Q13.1) WILD-TYPE                                     378
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 32(14Q13.1) MUTATED                               5
  DEL PEAK 32(14Q13.1) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 32(14Q13.1) MUTATED                                  42
  DEL PEAK 32(14Q13.1) WILD-TYPE                                71
D82V3, multiclass
                                         clus
vv                                        DEL PEAK 32(14Q13.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           26
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 42
                                         clus
vv                                        DEL PEAK 32(14Q13.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            378
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(14Q13.1) MUTATED    46   3   2   5
  DEL PEAK 32(14Q13.1) WILD-TYPE 325  19  14  35
D82V4, multiclass
    clus
vv   DEL PEAK 32(14Q13.1) MUTATED DEL PEAK 32(14Q13.1) WILD-TYPE
  R0                           46                            325
  R1                            3                             19
  R2                            2                             14
  RX                            5                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(83) Variable = DEL PEAK 33(15Q15.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q15.1) MUTATED   102  37
  DEL PEAK 33(15Q15.1) WILD-TYPE 345  53
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                           139                            398 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                            37                             53 
$`DEL PEAK 33(15Q15.1) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AX-A06B TCGA-AX-A1CR 
       29.39        20.81        10.19       110.63        67.66        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 
       61.18        27.88         1.38        80.38        27.09        66.41 
TCGA-BG-A0YV TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-KP-A3VZ 
       12.56        33.30        10.19        14.40        17.92        23.74 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       65.75        60.53        37.91        17.59        31.99        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK 
      118.19        66.15        28.64        25.51        14.96        18.41 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF 
       21.14        34.16        18.90         1.64        22.26        21.21 
TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A1DQ 
       16.87        20.78        21.99        45.53        97.71        46.78 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A060 TCGA-AX-A0IW TCGA-AX-A1C9 
       21.90        36.13         0.56        35.34        37.78        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO 
       32.02        25.91        76.83        30.12         2.96        64.93 
TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
        0.23         0.20        20.52         0.30         0.26         0.39 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU 
       27.29        27.85        75.72        52.04       102.31        50.89 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A18C 
       11.87        31.36       136.60        29.65        34.95        15.45 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       31.00        24.13        16.64        61.87        92.88        83.64 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       29.95         8.55        22.55        37.32        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 
       18.67         3.95        14.73        13.22         0.72         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DI-A1NN 
        4.27        18.84        17.29        71.61       109.08        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        9.37        31.10       110.10        79.10        10.92        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       51.42        19.40        34.39        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW 
       16.34        54.15        19.27        18.84        22.03        11.08 
TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       12.59        20.05        45.76        29.10        27.35        11.38 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       77.33        96.69        59.01        28.93        30.67        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
       41.56        78.38        14.04        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       23.24        38.70        22.59         8.19         4.44        20.75 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 33(15Q15.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-BG-A0M6 
       57.80        93.99        95.47        12.26        36.39        22.06 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       61.87        51.55        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 
       47.84        16.93         6.21        22.78        17.88        18.87 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 
       19.89         5.88        66.77        13.84        73.32        36.00 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
        0.43        39.52        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
       15.95        31.99        33.07        24.72        34.95        11.21 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       20.25        14.43        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       18.12        33.90        14.66        22.49        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       20.65        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82         2.70        35.11         0.13       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T 
       60.23        45.86        27.85        51.12        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 
       29.69        80.55        88.24        71.51        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       34.65        25.51        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58         4.77        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT 
       46.49        38.24        17.75        30.74        31.13         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.56        43.82         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       64.21        63.55        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57       225.50        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
       52.54        96.30        93.50        71.84        39.35        27.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
       22.39        35.90        34.98        35.90        35.08        31.76 
TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.99        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       66.48        16.83         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KU 
       48.79         8.48        58.95        15.88         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        12.39        23.38        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
       45.57        16.04         7.36        16.80        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        51.52        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       35.15        38.07        46.42        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        32.71        17.62        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 
       37.05        19.33        22.82        31.04        32.52        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.70        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A916 
        9.34         1.74        17.75         9.47        21.30        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE 
                         26.37                          32.04 
[1] "0.1 - 136.6 (26.4)" "0.1 - 225.5 (32.0)"
[1] "hr=" "2.3"
D83V2, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.1) MUTATED    76  53
  DEL PEAK 33(15Q15.1) WILD-TYPE 214 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.1) MUTATED     76   53
  DEL PEAK 33(15Q15.1) WILD-TYPE  214  171
     clus
vv    DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  NO                            76                            214
  YES                           53                            171
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 33(15Q15.1) MUTATED                                        54
  DEL PEAK 33(15Q15.1) WILD-TYPE                                     350
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 33(15Q15.1) MUTATED                              10
  DEL PEAK 33(15Q15.1) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 33(15Q15.1) MUTATED                                  76
  DEL PEAK 33(15Q15.1) WILD-TYPE                                37
D83V3, multiclass
                                         clus
vv                                        DEL PEAK 33(15Q15.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           54
  MIXED SEROUS AND ENDOMETRIOID                                     10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 76
                                         clus
vv                                        DEL PEAK 33(15Q15.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            350
  MIXED SEROUS AND ENDOMETRIOID                                       12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q15.1) MUTATED    86   7   7  15
  DEL PEAK 33(15Q15.1) WILD-TYPE 285  15   9  25
D83V4, multiclass
    clus
vv   DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
  R0                           86                            285
  R1                            7                             15
  R2                            7                              9
  RX                           15                             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(84) Variable = DEL PEAK 34(15Q23) MUTATION ANALYSIS
D84V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 34(15Q23) MUTATED    89  26
  DEL PEAK 34(15Q23) WILD-TYPE 358  64
  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                         115                          422 
  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                          26                           64 
$`DEL PEAK 34(15Q23) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2H8 
       29.39        20.81        10.19        67.66        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-E6-A8L9 
       27.88         1.38        80.38        27.09        66.41        33.30 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN 
       10.19        14.40        17.92        23.74        65.75        60.53 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       37.91        17.59        31.99       118.19        66.15        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD 
       25.51        14.96        18.41        14.43        21.14        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS 
       18.12        18.90         1.64        22.26        21.21        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       16.87        20.78        21.99        45.53        48.79       125.42 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA 
       21.90        36.13         0.56        37.78        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FZ 
       25.91        30.12         2.96        64.93         0.23         0.20 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P 
        0.26         0.30         0.39        27.85        75.72        52.04 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3S1 TCGA-BG-A0MT 
      102.31        11.87        31.36       136.60        29.65        21.17 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
       15.45        22.39        24.13        16.64        61.87        92.88 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
        8.55        22.55        11.51        31.07        18.67         3.95 
TCGA-D1-A1NU TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-EO-A1Y5 
       13.22        18.84        17.29         9.37        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       37.71        51.42        19.40        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A2OO 
       16.34        54.15        19.27        18.84        22.03        45.76 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       27.35        11.38        14.70        77.33        96.69        59.01 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 
       28.93        30.67         1.74        17.75        14.04        13.28 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       26.10        23.24        38.70        22.59         8.19         4.44 
TCGA-SJ-A6ZI 
       20.75 

$`DEL PEAK 34(15Q23) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        93.99        95.47        12.26        36.39 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        16.93         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        18.87        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      105.37       123.68        74.10        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        36.33        33.07 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL 
       24.72        34.95        11.21        20.25        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       35.15        34.36        33.90        14.66        22.49        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82         2.70        35.11         0.13       129.80 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.62        20.91       117.99       110.37        66.25        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T 
       60.23        45.86        27.85        51.12        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       61.08        35.74        43.82        40.11        77.39        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       32.91        34.65        25.51        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       73.41        80.25        37.58         4.77        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       31.13         0.20         0.56        43.82        20.52         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       59.24        86.01        58.75        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      225.50        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        93.50        71.84        39.35        27.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU 
       48.56        23.47        43.30        43.04        59.74        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98        35.90        35.08        31.00        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83        29.95         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN TCGA-DF-A2KR 
        8.48        58.95        15.88         4.27         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT 
       16.31        39.29        36.62        24.30        35.38        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10       110.10        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       35.15        38.07        46.42        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        32.71        17.62        16.11        32.78        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY 
       31.04        29.10        32.52        14.14        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-FI-A3PV 
       39.88         7.99        25.22         9.34        59.28        41.56 
TCGA-FI-A3PX TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       78.38         9.47        18.21        21.30        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZJ 
       22.65        39.95        24.95        23.64        14.83        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                        0.20                         0.07 
  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                       136.6                        225.5 
  DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE 
                      22.550                       32.745 
[1] "0.2 - 136.6 (22.6)" "0.1 - 225.5 (32.7)"
[1] "hr=" "1.9"
D84V2, binary
                              cls
clus                             0   1
  DEL PEAK 34(15Q23) MUTATED    56  51
  DEL PEAK 34(15Q23) WILD-TYPE 234 173
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 34(15Q23) MUTATED     56   51
  DEL PEAK 34(15Q23) WILD-TYPE  234  173
     clus
vv    DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE
  NO                          56                          234
  YES                         51                          173
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 34(15Q23) MUTATED                                        38
  DEL PEAK 34(15Q23) WILD-TYPE                                     366
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 34(15Q23) MUTATED                               8
  DEL PEAK 34(15Q23) WILD-TYPE                            14
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 34(15Q23) MUTATED                                  69
  DEL PEAK 34(15Q23) WILD-TYPE                                44
D84V3, multiclass
                                         clus
vv                                        DEL PEAK 34(15Q23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         38
  MIXED SEROUS AND ENDOMETRIOID                                    8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               69
                                         clus
vv                                        DEL PEAK 34(15Q23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          366
  MIXED SEROUS AND ENDOMETRIOID                                     14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 34(15Q23) MUTATED    78   4   5   9
  DEL PEAK 34(15Q23) WILD-TYPE 293  18  11  31
D84V4, multiclass
    clus
vv   DEL PEAK 34(15Q23) MUTATED DEL PEAK 34(15Q23) WILD-TYPE
  R0                         78                          293
  R1                          4                           18
  R2                          5                           11
  RX                          9                           31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(85) Variable = DEL PEAK 35(16P13.3) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16P13.3) MUTATED    64  27
  DEL PEAK 35(16P13.3) WILD-TYPE 383  63
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            91                            446 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            27                             63 
$`DEL PEAK 35(16P13.3) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A3G3 
       29.39        20.81        10.19        67.66        23.05         1.38 
TCGA-B5-A0KB TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       27.09        16.93        33.30        10.19        36.00        23.74 
TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO 
       37.02        60.53        31.99        36.33        28.64        25.51 
TCGA-AJ-A23M TCGA-AJ-A3BF TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 
       20.25        18.12        16.87        21.99        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A1C8 
      125.42        97.71        46.78        21.90         0.56        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       26.37        25.91        76.83         4.77        30.12        71.24 
TCGA-AX-A2IO TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K8 
       64.93         0.26         0.39        55.30        27.29        27.85 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A3S1 
       75.72        52.04       102.31        11.87        39.35        29.65 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD 
       34.95        15.45        22.39        35.08        31.00        16.64 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU 
       83.64        22.55        11.51        31.07        18.67        13.22 
TCGA-D1-A1NW TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2L0 TCGA-DI-A1NN 
        0.72         4.27        18.84        17.29        25.91        35.38 
TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
        9.37       110.10        10.92        49.15        37.71        51.42 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 
       27.16        26.96        17.62        12.59        29.10        27.35 
TCGA-EY-A3QX TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       32.52        96.69        28.93        41.56        78.38         1.74 
TCGA-JU-AAVI TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       17.75        18.21        23.24        38.70         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 35(16P13.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        57.80        93.99        95.47        12.26        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS 
       61.18        27.88        80.38        22.06        66.41        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 
       47.84         6.21        22.78        17.88        14.40        18.87 
TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       17.92        19.89         5.88        66.77        13.84        73.32 
TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
        0.43        39.52        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37       123.68        74.10 
TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        37.91        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 
       29.06        42.35        15.95        31.99        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       66.15        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        21.14        19.79        35.15        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.16        18.90        33.90         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07        48.03        63.91        36.89        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        66.25        36.36        46.72 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ 
       83.97        27.12        82.52        33.40        61.64        80.78 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        90.97        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       51.12        36.13        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       34.65        32.02        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       37.58        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74         2.96        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.56        43.82         0.20        20.52         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18        18.35        14.47        56.91        86.37        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       72.62        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        88.34        54.44        73.64        61.68 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       85.78        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       225.50        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       51.45        14.70        48.43        52.54        31.36       136.60 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        93.50        71.84        27.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       14.83        13.78        14.73        14.01        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       35.90        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KS 
        8.48        58.95        15.88         2.20        71.61       109.08 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30        12.39        31.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       19.40        34.39        50.73        35.15        38.07        46.42 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        16.34        38.47        51.09        14.99        54.15 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT 
       33.34        32.71        19.27        18.84        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       32.78        15.81        11.08        37.05        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A 
       20.05        45.76        31.04        11.38        14.14        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       16.96        68.38        39.88        77.33         7.99        25.22 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 
       59.01         9.34        30.67        59.28        14.04        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
        9.47        26.10        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                        125.42                         225.50 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                         27.09                          30.89 
[1] "0.1 - 125.4 (27.1)" "0.1 - 225.5 (30.9)"
[1] "hr=" "2.5"
D85V2, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    48  36
  DEL PEAK 35(16P13.3) WILD-TYPE 242 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     48   36
  DEL PEAK 35(16P13.3) WILD-TYPE  242  188
     clus
vv    DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  NO                            48                            242
  YES                           36                            188
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                                        27
  DEL PEAK 35(16P13.3) WILD-TYPE                                     377
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 35(16P13.3) MUTATED                               5
  DEL PEAK 35(16P13.3) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                                  60
  DEL PEAK 35(16P13.3) WILD-TYPE                                53
D85V3, multiclass
                                         clus
vv                                        DEL PEAK 35(16P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           27
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 60
                                         clus
vv                                        DEL PEAK 35(16P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            377
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16P13.3) MUTATED    55   6   4   9
  DEL PEAK 35(16P13.3) WILD-TYPE 316  16  12  31
D85V4, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  R0                           55                            316
  R1                            6                             16
  R2                            4                             12
  RX                            9                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(86) Variable = DEL PEAK 36(16Q21) MUTATION ANALYSIS
D86V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 36(16Q21) MUTATED   116  37
  DEL PEAK 36(16Q21) WILD-TYPE 331  53
  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                         153                          384 
  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                          37                           53 
$`DEL PEAK 36(16Q21) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B 
       29.39        10.19       110.63        57.80        93.99        67.66 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB 
       36.39        23.05        61.18        27.88         1.38        27.09 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 
       22.06        66.41        51.55        12.56        16.93        33.30 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       10.19        14.40        17.92        36.00        23.74        39.52 
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
      123.68        65.75        60.53        17.59        31.99        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M 
      118.19        28.64        25.51        14.96        18.41        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3TW 
       14.43        21.14        34.16        22.26        21.21        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI 
       20.78        21.99        45.53        36.89        48.79        97.71 
TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A05U TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       46.78         0.56        29.69        35.74        37.78        34.65 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A2H4 
       26.37        32.02        25.91        85.48        37.58        30.12 
TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX 
       71.24        46.49         2.96        64.93         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.20        20.52         0.30         0.26         0.30         0.39 
TCGA-B5-A0JT TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P 
       55.30        64.21        27.85       113.36        75.72        52.04 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE 
      102.31        11.87        31.36        39.35        29.65        34.95 
TCGA-BG-A0MU TCGA-BG-A0VW TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A4ZD 
       20.28        52.01        13.78        15.45        23.70        16.64 
TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I 
       61.87        83.64        22.55        39.48        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NU 
       29.92        31.07        14.73        28.08        11.15        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ 
        0.72        18.25         2.07         4.27        18.84        17.29 
TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
      109.08        25.91        35.38         9.37        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       79.10        10.92        49.15        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       34.39        27.16        26.96        22.26        16.34        54.15 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 
       23.90        32.71        17.62        22.03        15.81        12.59 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY 
       29.10        27.35        32.52        11.38        14.70        68.38 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       96.69        59.01         9.34        28.93        30.67        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A915 
       78.38         1.74        26.10        18.21        38.70         8.19 
TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44         0.07         0.23 

$`DEL PEAK 36(16Q21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A0LS TCGA-AX-A06D TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A220 
       20.81        95.47        12.26        80.38        61.87        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
        1.81        19.79         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        18.87        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       73.32         0.43        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        73.87        36.82        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        37.91        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       15.95        31.99        33.07        66.15        24.72        34.95 
TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       11.21        10.26        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90        33.90         1.64        14.66        22.49        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       16.87        22.32        12.82         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
      129.80        23.31        86.07        48.03        63.91        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.62        20.91       125.42       117.99       110.37        66.25 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        31.30        35.54        49.15         6.71        60.23 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       45.86        27.85        51.12        21.90        36.13        13.58 
TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       33.21        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       61.08        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 
       25.51        34.09        76.83        73.41        80.25         4.77 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       40.80        81.37        34.32        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       31.13         0.23         0.20         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        86.37        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J 
       63.55        13.45        59.84       185.79        88.34        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      225.50        50.89        51.45        14.70        48.43        52.54 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
      136.60        96.30        93.50        71.84        27.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY 
       23.47        43.30        43.04        59.74        21.17        15.42 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       51.06        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.73        14.01        15.45         9.57        20.02        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 
       77.95        67.99        96.49        30.74        97.41        92.88 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.36        37.51        36.79        33.63        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       15.88         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT 
       27.16        16.31        39.29        36.62        24.30        12.39 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX 
       51.52        50.73        35.15        38.07        46.42        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       51.09        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        33.34        19.27        18.84        16.11        32.78 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       11.08        37.05        19.33        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       31.04        14.14        16.96        39.88        77.33         7.99 
TCGA-FI-A2D6 TCGA-FI-A2F9 TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       25.22        59.28        17.75        14.04        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        21.30        22.59        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 

  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                        0.07                         0.13 
  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                      123.68                       225.50 
  DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE 
                       27.85                        31.02 
[1] "0.1 - 123.7 (27.9)" "0.1 - 225.5 (31.0)"
[1] "hr=" "1.9"
D86V2, binary
                              cls
clus                             0   1
  DEL PEAK 36(16Q21) MUTATED    80  61
  DEL PEAK 36(16Q21) WILD-TYPE 210 163
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(16Q21) MUTATED     80   61
  DEL PEAK 36(16Q21) WILD-TYPE  210  163
     clus
vv    DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE
  NO                          80                          210
  YES                         61                          163
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 36(16Q21) MUTATED                                        65
  DEL PEAK 36(16Q21) WILD-TYPE                                     339
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 36(16Q21) MUTATED                               9
  DEL PEAK 36(16Q21) WILD-TYPE                            13
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 36(16Q21) MUTATED                                  80
  DEL PEAK 36(16Q21) WILD-TYPE                                33
D86V3, multiclass
                                         clus
vv                                        DEL PEAK 36(16Q21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         65
  MIXED SEROUS AND ENDOMETRIOID                                    9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               80
                                         clus
vv                                        DEL PEAK 36(16Q21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          339
  MIXED SEROUS AND ENDOMETRIOID                                     13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 36(16Q21) MUTATED    98   8   7  12
  DEL PEAK 36(16Q21) WILD-TYPE 273  14   9  28
D86V4, multiclass
    clus
vv   DEL PEAK 36(16Q21) MUTATED DEL PEAK 36(16Q21) WILD-TYPE
  R0                         98                          273
  R1                          8                           14
  R2                          7                            9
  RX                         12                           28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(87) Variable = DEL PEAK 37(16Q22.3) MUTATION ANALYSIS
D87V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16Q22.3) MUTATED   123  34
  DEL PEAK 37(16Q22.3) WILD-TYPE 324  56
  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                           157                            380 
  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                            34                             56 
$`DEL PEAK 37(16Q22.3) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       29.39        10.19        57.80        93.99        67.66        36.39 
TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 
       23.05        61.18        27.88         1.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A0YV TCGA-D1-A3JP TCGA-EY-A1GK TCGA-EY-A214 
       66.41        51.55        12.56        16.93        22.78        14.40 
TCGA-EY-A547 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G5 
       17.92         5.88        36.00        23.74        39.52        37.02 
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
      123.68        65.75        60.53        36.82        37.91        17.59 
TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK 
       31.99       118.19        28.64        25.51        14.96        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       20.25        14.43        21.14        34.16        18.12        18.90 
TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A 
       22.26        21.21        16.87        20.78        21.99        63.91 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A05U 
       36.89        48.79        97.71        46.78         0.56        29.69 
TCGA-AX-A05Y TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       88.24        35.74        34.65        25.51        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       25.91        76.83        85.48        37.58        30.12        71.24 
TCGA-AX-A2HD TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       46.49         2.96        64.93         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT 
       20.52         0.30         0.26         0.30         0.39        55.30 
TCGA-B5-A0K6 TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY 
       64.21       113.36        75.72        52.04       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0MU TCGA-BG-A0VW TCGA-BG-A186 
       31.36        39.35        34.95        20.28        52.01        13.78 
TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI 
       15.45        23.70        35.08        24.13        16.64        61.87 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       83.64        22.55        27.42        11.51        29.92        31.07 
TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NU 
       18.67        14.73        28.08        10.22        11.15        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ 
        0.72        18.25         2.07         4.27        18.84        17.29 
TCGA-DF-A2KR TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
       71.61        25.91        35.38         9.37        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       79.10        10.92        37.71        51.42        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM 
       27.16        26.96        22.26        16.34        54.15        32.71 
TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       17.62        15.81        12.59        29.10        27.35        32.52 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       14.70        68.38        96.69        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W0 TCGA-KP-A3W3 
       30.67        59.28        41.56        78.38        13.28        26.10 
TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       18.21        38.70        22.59         8.19         4.44         0.07 
TCGA-SL-A6JA 
        0.23 

$`DEL PEAK 37(16Q22.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06D TCGA-B5-A0JN TCGA-BG-A0MS 
       20.81       110.63        95.47        12.26        80.38        61.87 
TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 
       14.27         1.81        19.79         4.44        47.84        33.30 
TCGA-EY-A1G7 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX 
        6.21        17.88        10.19        18.87        19.89        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       13.84        73.32         0.43        10.29       106.88       149.56 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       83.51        17.85        32.78       112.54       105.37        74.10 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        73.87        28.27        54.02        23.21        68.65 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
       36.33        33.07        66.15        24.72        34.95        11.21 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       10.26        19.79        35.15        34.36        33.90         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       48.03        45.53        23.87        12.62        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        36.36        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Z 
       21.90        36.13        13.58        33.21        80.55        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        61.08        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CK 
       77.39        13.28        32.91        34.09        73.41        80.25 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH 
        4.77        40.80        81.37        34.32        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 
       30.74        31.13         0.23         0.20         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        86.37        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        54.44        73.64        61.68        85.78        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       77.23        73.28        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       225.50        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54       136.60        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        29.65        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       59.74        21.17        15.42        51.06        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.83        56.58        14.83        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
        9.57        20.02        20.12        11.31        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.90        31.00        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        89.59        63.58        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16O 
       36.10        37.32        36.36        37.51        36.79        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q 
       30.44         1.28        28.01        26.37         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       15.88         2.20       109.08       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT 
       27.16        16.31        39.29        36.62        24.30        12.39 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        49.15        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       57.60        51.52        50.73        35.15        38.07        46.42 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        23.90        33.34        19.27        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       22.03        16.11        32.78        11.08        37.05        19.33 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A548 
       22.82        20.05        45.76        31.04        11.38        14.14 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-H5-A2HR 
       16.96        39.88        77.33         7.99        25.22         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 
       17.75        14.04         9.47        23.24        21.30        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       20.75        18.28 

  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                        123.68                         225.50 
  DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE 
                        27.160                         31.085 
[1] "0.1 - 123.7 (27.2)" "0.1 - 225.5 (31.1)"
[1] "hr=" "1.6"
D87V2, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q22.3) MUTATED    83  63
  DEL PEAK 37(16Q22.3) WILD-TYPE 207 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q22.3) MUTATED     83   63
  DEL PEAK 37(16Q22.3) WILD-TYPE  207  161
     clus
vv    DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE
  NO                            83                            207
  YES                           63                            161
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 37(16Q22.3) MUTATED                                        69
  DEL PEAK 37(16Q22.3) WILD-TYPE                                     335
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 37(16Q22.3) MUTATED                               9
  DEL PEAK 37(16Q22.3) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 37(16Q22.3) MUTATED                                  80
  DEL PEAK 37(16Q22.3) WILD-TYPE                                33
D87V3, multiclass
                                         clus
vv                                        DEL PEAK 37(16Q22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           69
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 80
                                         clus
vv                                        DEL PEAK 37(16Q22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            335
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(16Q22.3) MUTATED   102   9   7  13
  DEL PEAK 37(16Q22.3) WILD-TYPE 269  13   9  27
D87V4, multiclass
    clus
vv   DEL PEAK 37(16Q22.3) MUTATED DEL PEAK 37(16Q22.3) WILD-TYPE
  R0                          102                            269
  R1                            9                             13
  R2                            7                              9
  RX                           13                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(88) Variable = DEL PEAK 38(16Q23.1) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16Q23.1) MUTATED   126  39
  DEL PEAK 38(16Q23.1) WILD-TYPE 321  51
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                           165                            372 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                            39                             51 
$`DEL PEAK 38(16Q23.1) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A0LF TCGA-AX-A06B TCGA-AX-A1CP 
       29.39        10.19        57.80        93.99        67.66        36.39 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT 
       27.88         1.38        27.09        22.06        66.41        51.55 
TCGA-BG-A0YV TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1GK TCGA-EY-A214 TCGA-EY-A547 
       12.56        16.93        33.30        22.78        14.40        17.92 
TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ 
        5.88        36.00        23.74        39.52       123.68        65.75 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 
       60.53        36.82        37.91        17.59        31.99       118.19 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       28.64        25.51        14.96        18.41        20.25        14.43 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3TW 
       21.14        34.16        18.12        22.26        21.21        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       20.78        21.99        63.91        45.53        36.89        48.79 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06F TCGA-AX-A0IU 
       97.71        46.78        29.69        88.24        57.47        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       37.78        34.65        25.51        26.37        32.02        25.91 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       76.83        85.48        37.58         4.77        30.12        71.24 
TCGA-AX-A2HD TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       46.49         2.96        64.93         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT 
       20.52         0.30         0.26         0.30         0.39        55.30 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
       27.29        64.21       113.36        75.72        52.04       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0MU 
       11.87        31.36        39.35        29.65        34.95        20.28 
TCGA-BG-A0VW TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L 
       52.01        13.78        15.45        23.70        35.08        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V 
       16.64         4.80        61.87        83.64        22.55        39.48 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K 
       27.42        29.92        31.07        18.67        14.73        28.08 
TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       10.22        11.15        13.22         0.72        18.25        16.87 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2L0 
        2.07         4.27        18.84        17.29        71.61        25.91 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
       35.38         9.37        31.10       110.10        79.10        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 
       37.71        51.42        19.40        34.39        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       22.26        16.34        54.15        32.71        17.62        22.03 
TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       15.81        12.59        20.05        29.10        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       11.38        14.70        68.38        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        30.67        59.28        41.56        78.38         1.74 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       13.28        26.10        18.21        38.70        22.59         8.19 
TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44         0.07         0.23 

$`DEL PEAK 38(16Q23.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CR TCGA-AX-A2H8 
       20.81       110.63        95.47        12.26        23.05        61.18 
TCGA-B5-A0JN TCGA-BG-A0MS TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       80.38        61.87        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 
       47.84         6.21        17.88        10.19        18.87        19.89 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       66.77        13.84        73.32         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
      105.37        74.10        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95        31.99        36.33        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       34.95        11.21        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90        33.90         1.64        14.66        22.49        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       16.87        22.32        12.82         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O 
      129.80        23.31        86.07        48.03        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        66.25        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       46.72        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       80.78        49.22        25.08        71.67        90.97        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       31.30        35.54        49.15         6.71        60.23        45.86 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        51.12        21.90        36.13         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       33.21        80.55        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       49.87        27.39        30.02        60.66        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CE TCGA-AX-A1CJ 
       40.11        77.39        13.28        32.91        34.09        73.41 
TCGA-AX-A1CK TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH 
       80.25        40.80        81.37        34.32        38.24        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 
       30.74        31.13         0.23         0.20         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        86.37        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       69.27        71.44        48.59        36.49        72.62        57.76 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H 
       63.55        27.85        13.45        59.84       185.79        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       225.50        50.89        51.45        14.70        48.43 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       52.54       136.60        96.30        93.50        71.84        27.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       15.42        51.06        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       14.83        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31        22.39        35.90        34.98        35.90 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.00        31.76        24.99        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TJ 
       46.95        24.33        85.55        78.21        77.95        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       96.49        30.74        97.41        92.88       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       36.79        11.51        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       26.37         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
        1.41        18.02        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU 
        8.48        58.95        15.88         2.20       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        12.39        23.38        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       66.90        46.26        57.60        51.52        50.73        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD 
       38.07        46.42        38.47        51.09        14.99        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
       19.27        18.84        16.11        32.78        11.08        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A5W2 
       19.33        22.82        45.76        31.04        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-JU-AAVI TCGA-K6-A3WQ 
       39.88        77.33         7.99        25.22        17.75        14.04 
TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.47        23.24        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        24.95        23.64        14.83        20.75        18.28 

  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                        123.68                         225.50 
  DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE 
                        27.290                         31.215 
[1] "0.1 - 123.7 (27.3)" "0.1 - 225.5 (31.2)"
[1] "hr=" "2"  
D88V2, binary
                                cls
clus                               0   1
  DEL PEAK 38(16Q23.1) MUTATED    88  65
  DEL PEAK 38(16Q23.1) WILD-TYPE 202 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16Q23.1) MUTATED     88   65
  DEL PEAK 38(16Q23.1) WILD-TYPE  202  159
     clus
vv    DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  NO                            88                            202
  YES                           65                            159
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                        71
  DEL PEAK 38(16Q23.1) WILD-TYPE                                     333
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 38(16Q23.1) MUTATED                               8
  DEL PEAK 38(16Q23.1) WILD-TYPE                            14
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 38(16Q23.1) MUTATED                                  87
  DEL PEAK 38(16Q23.1) WILD-TYPE                                26
D88V3, multiclass
                                         clus
vv                                        DEL PEAK 38(16Q23.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           71
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 87
                                         clus
vv                                        DEL PEAK 38(16Q23.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            333
  MIXED SEROUS AND ENDOMETRIOID                                       14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16Q23.1) MUTATED   105   8  10  14
  DEL PEAK 38(16Q23.1) WILD-TYPE 266  14   6  26
D88V4, multiclass
    clus
vv   DEL PEAK 38(16Q23.1) MUTATED DEL PEAK 38(16Q23.1) WILD-TYPE
  R0                          105                            266
  R1                            8                             14
  R2                           10                              6
  RX                           14                             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(89) Variable = DEL PEAK 39(17P13.3) MUTATION ANALYSIS
D89V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P13.3) MUTATED    84  37
  DEL PEAK 39(17P13.3) WILD-TYPE 363  53
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                           121                            416 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                            37                             53 
$`DEL PEAK 39(17P13.3) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CR 
       41.06        10.19       110.63        57.80        67.66        23.05 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 
       61.18        27.88         1.38        80.38        27.09        22.06 
TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A547 TCGA-KJ-A3U4 
       66.41        16.93        33.30        10.19        17.92        36.00 
TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG 
       23.74        39.52        65.75        60.53        37.91        31.99 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF 
       28.64        25.51        14.43        21.14        34.16        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       18.90         1.64        17.06        16.87        16.87        20.78 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A1DQ 
       21.99        45.53        48.79       125.42        36.36        46.78 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       21.90        36.13         0.56        35.74        37.78        34.65 
TCGA-AX-A1C8 TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       25.51        17.75        64.93         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 
       20.52         0.30         0.26         0.39        27.29        27.85 
TCGA-B5-A11I TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
       75.72        61.68       102.31        11.87        31.36       136.60 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L 
       39.35        29.65        15.45        22.39        31.00        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ 
       16.64        61.87        92.88        83.64        29.95        22.55 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW 
       39.48        37.32        31.07        18.67        13.22         0.72 
TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU 
       17.29       109.08        25.91        35.38         9.37        31.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU 
       10.92        49.15        37.71        51.42        19.40        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
       16.34        23.90        32.71        17.62        22.03        11.08 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY 
       29.10        11.38        14.70        68.38        77.33        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       30.67        41.56        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A917 TCGA-QS-A8F1 
       13.28        23.24        38.70         8.19         6.97         4.44 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 39(17P13.3) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP TCGA-BG-A0MS 
       20.81        93.99        95.47        12.26        36.39        61.87 
TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 
       51.55        12.56        14.27         1.81        19.79         4.44 
TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 
       47.84         6.21        22.78        17.88        14.40        18.87 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E 
       19.89         5.88        66.77        13.84        73.32         0.43 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP 
       32.78       112.54       105.37       123.68        74.10        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 
       31.99        36.33        33.07       118.19        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O 
       34.95        14.96        11.21        18.41        20.25        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       19.79        35.15        34.36        33.90        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.26        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV 
       15.95        14.76        22.32        12.82         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13       129.80        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.62        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        97.71        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T 
       60.23        45.86        27.85        51.12        13.58        33.21 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        80.55        88.24        71.51        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       79.46        49.87        57.47        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       61.08        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       73.41        80.25        37.58         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       40.80        81.37        34.32        46.49        38.24        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G7 TCGA-AX-A3G8 
        2.96        31.13         0.23         0.20         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       72.62        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O 
      185.79       113.36        88.34        54.44        73.64        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       225.50        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       51.45        14.70        48.43        52.54        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       71.84        27.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98        35.90 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       35.08        31.76        24.99        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.58        86.99        66.48        16.83         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W 
        4.87        28.67        23.93         1.74        21.99        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       29.88         1.91         3.68        29.33        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       11.51        29.92        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92         1.41        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       48.79         8.48        58.95        15.88         4.27        18.84 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20        71.61       100.83        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.36        16.80        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        38.47        51.09        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       54.15        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        19.27        18.84        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2D0 
       31.04        27.35        32.52        14.14        16.96        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 
        7.99        25.22        96.69        59.01         9.34        59.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
        9.47        26.10        18.21        21.30        22.59        17.16 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE 
                         27.09                          30.74 
[1] "0.1 - 136.6 (27.1)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.7"
D89V2, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P13.3) MUTATED    59  51
  DEL PEAK 39(17P13.3) WILD-TYPE 231 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P13.3) MUTATED     59   51
  DEL PEAK 39(17P13.3) WILD-TYPE  231  173
     clus
vv    DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  NO                            59                            231
  YES                           51                            173
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                                        48
  DEL PEAK 39(17P13.3) WILD-TYPE                                     356
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 39(17P13.3) MUTATED                               9
  DEL PEAK 39(17P13.3) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 39(17P13.3) MUTATED                                  65
  DEL PEAK 39(17P13.3) WILD-TYPE                                48
D89V3, multiclass
                                         clus
vv                                        DEL PEAK 39(17P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           48
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 65
                                         clus
vv                                        DEL PEAK 39(17P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            356
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17P13.3) MUTATED    73   7   4  14
  DEL PEAK 39(17P13.3) WILD-TYPE 298  15  12  26
D89V4, multiclass
    clus
vv   DEL PEAK 39(17P13.3) MUTATED DEL PEAK 39(17P13.3) WILD-TYPE
  R0                           73                            298
  R1                            7                             15
  R2                            4                             12
  RX                           14                             26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(90) Variable = DEL PEAK 40(17P11.2) MUTATION ANALYSIS
D90V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P11.2) MUTATED    89  38
  DEL PEAK 40(17P11.2) WILD-TYPE 358  52
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           127                            410 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                            38                             52 
$`DEL PEAK 40(17P11.2) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A1CR 
       41.06        20.81        10.19       110.63        57.80        23.05 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-D1-A3JP TCGA-E6-A8L9 
       27.88         1.38        27.09        66.41        16.93        33.30 
TCGA-EY-A212 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ 
       10.19        17.92        36.00        23.74        39.52        65.75 
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       60.53        36.82        37.91        31.99        36.33       118.19 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       28.64        25.51        18.41        20.25        14.43        21.14 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3QS 
       18.12        18.90         1.64        17.06        21.21        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       16.87        20.78        63.91        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IU 
      125.42        36.36        97.71        46.78         0.56        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 
       37.78        34.65        25.51        76.83         4.77        71.24 
TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       17.75        64.93         0.56        43.82         0.20        20.52 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 
        0.26         0.30         1.18         0.39        27.29        27.85 
TCGA-B5-A11I TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       75.72        61.68       102.31        50.89        11.87        31.36 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
      136.60        39.35        15.45        31.00        24.13        16.64 
TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16I 
       92.88        29.95        22.55        39.48        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A2G7 
       31.07        18.67        13.22         0.72        18.25        58.95 
TCGA-D1-A3DH TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NN TCGA-DI-A1NO 
       18.84        71.61       109.08        25.91        35.38         9.37 
TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       31.10        79.10        10.92        49.15        37.71        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GW 
       19.40        34.39        22.26        32.71        17.62        11.08 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       11.38        14.70        68.38        77.33         9.34        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       30.67        59.28        41.56        78.38         1.74        17.75 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       14.04        13.28        23.24        38.70         8.19         4.44 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 40(17P11.2) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 
       93.99        95.47        67.66        12.26        36.39        61.18 
TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       80.38        22.06        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-EY-A1G7 TCGA-EY-A1GK 
        1.81        19.79         4.44        47.84         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       17.88        14.40        18.87        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       13.84        73.32         0.43        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
      123.68        74.10        46.55        73.87        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 
       42.35        15.95        31.99        33.07        66.15        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
       34.95        14.96        11.21        10.26        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       34.36        34.16        33.90        14.66        22.49        22.26 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O 
       21.99        23.31        86.07        48.03        23.87        12.62 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
       20.91       117.99       110.37        66.25        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       57.47        27.39        30.02        60.66        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        77.39        13.28        32.91        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       25.91        34.09        85.48        73.41        80.25        37.58 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       30.12        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G4 
       30.74         2.96        31.13         0.23         0.20         0.30 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       72.62        57.76        64.21        63.55        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O 
      185.79       113.36        88.34        54.44        73.64        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57       225.50        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        48.43        52.54        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       27.65        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD 
       13.78        14.73        14.01        15.45         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31        22.39        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       35.90        35.08        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       59.51        89.59        63.58        83.64        86.99        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       16.83         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
        3.95        48.79         8.48        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        2.20       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39       110.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       50.73        35.15        38.07        27.16        46.42        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 
       31.04        29.10        27.35        32.52        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-KP-A3W1 
       39.88         7.99        25.22        96.69        59.01         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       26.10        18.21        21.30        22.59        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                        27.850                         30.135 
[1] "0.1 - 136.6 (27.9)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.5"
D90V2, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    64  51
  DEL PEAK 40(17P11.2) WILD-TYPE 226 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     64   51
  DEL PEAK 40(17P11.2) WILD-TYPE  226  173
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  NO                            64                            226
  YES                           51                            173
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                        48
  DEL PEAK 40(17P11.2) WILD-TYPE                                     356
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 40(17P11.2) MUTATED                               9
  DEL PEAK 40(17P11.2) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                  71
  DEL PEAK 40(17P11.2) WILD-TYPE                                42
D90V3, multiclass
                                         clus
vv                                        DEL PEAK 40(17P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           48
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 71
                                         clus
vv                                        DEL PEAK 40(17P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            356
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P11.2) MUTATED    78   7   4  13
  DEL PEAK 40(17P11.2) WILD-TYPE 293  15  12  27
D90V4, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  R0                           78                            293
  R1                            7                             15
  R2                            4                             12
  RX                           13                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(91) Variable = DEL PEAK 41(17Q11.2) MUTATION ANALYSIS
D91V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(17Q11.2) MUTATED    75  29
  DEL PEAK 41(17Q11.2) WILD-TYPE 372  61
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           104                            433 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            29                             61 
$`DEL PEAK 41(17Q11.2) MUTATED`
TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A1CR TCGA-AX-A2H8 
       29.39        20.81        10.19        57.80        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-E6-A8L9 TCGA-EY-A212 
       27.88         1.38        22.06        66.41        33.30        10.19 
TCGA-EY-A547 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 
       17.92        23.74        65.75        60.53        37.91        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       31.99        36.33        25.51        20.25        14.43        21.14 
TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05A 
       18.90        22.26        17.06        16.87        21.99        63.91 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO 
       45.53        48.79       125.42        97.71        46.78         0.56 
TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2IO 
       37.78        25.51        76.83        30.12        71.24        64.93 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82         0.20        20.52         0.26         0.30 
TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD 
       61.68       102.31        31.36       136.60        39.35        34.13 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI 
       15.45        22.39        31.00        24.13        16.64        61.87 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       92.88        83.64        22.55        37.32        11.51        31.07 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DH 
       14.73        28.08        13.22         0.72         2.07        18.84 
TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QU 
       17.29        71.61       109.08        25.91         9.37        31.10 
TCGA-E6-A1LZ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       79.10        16.80        49.15        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GW 
       34.39        22.26        16.34        54.15        23.90        11.08 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F8 
       29.10        32.52        68.38        77.33        59.01        30.67 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A7D5 
       59.28         1.74        17.75        13.28        26.10        38.70 
TCGA-PG-A914 TCGA-QS-A8F1 
       22.59         4.44 

$`DEL PEAK 41(17Q11.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP 
      110.63        93.99        95.47        67.66        12.26        36.39 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 
       80.38        27.09        61.87        51.55        12.56        14.27 
TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 
        1.81        19.79         4.44        47.84        16.93         6.21 
TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D 
       22.78        17.88        14.40        18.87        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C 
       66.77        13.84        73.32        36.00         0.43        39.52 
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP 
       32.78       112.54       105.37       123.68        74.10        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       73.87        36.82        28.27        54.02        23.21        68.65 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95        31.99 
TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       33.07       118.19        66.15        28.64        24.72        34.95 
TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
       14.96        11.21        18.41        10.26        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        34.16        18.12        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.70        35.11         0.13       129.80        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       48.03        36.89        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        35.74        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       40.11        77.39        13.28        32.91        34.65        26.37 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       32.02        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58         4.77        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       38.24        17.75        30.74         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.20         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       57.76        64.21        63.55        27.85        13.45        59.84 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        73.64 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       85.78        52.04        32.09        77.23        73.28        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       19.56        19.50        18.41        17.36        16.57       225.50 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        51.45        14.70        48.43        11.87        52.54 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        93.50        71.84        27.65        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       71.24        63.68        74.63        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        59.74        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        51.06        52.01        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98        35.90        35.08        31.76        24.99        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
        4.80        77.95        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        48.79         8.48        58.95        15.88         4.27 
TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        2.20       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        24.30        35.38        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       26.96        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        27.35        11.38        14.14        14.70        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88         7.99        25.22        96.69         9.34        28.93 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
       41.56        78.38        14.04         9.47        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       21.30         8.19        17.16         6.97        22.65        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       24.95        23.64        14.83        20.75        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                         27.98                          30.08 
[1] "0.2 - 136.6 (28.0)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.1"
D91V2, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED    51  45
  DEL PEAK 41(17Q11.2) WILD-TYPE 239 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED     51   45
  DEL PEAK 41(17Q11.2) WILD-TYPE  239  179
     clus
vv    DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  NO                            51                            239
  YES                           45                            179
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                        46
  DEL PEAK 41(17Q11.2) WILD-TYPE                                     358
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 41(17Q11.2) MUTATED                               5
  DEL PEAK 41(17Q11.2) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                  54
  DEL PEAK 41(17Q11.2) WILD-TYPE                                59
D91V3, multiclass
                                         clus
vv                                        DEL PEAK 41(17Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           46
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 54
                                         clus
vv                                        DEL PEAK 41(17Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            358
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(17Q11.2) MUTATED    66   6   6  10
  DEL PEAK 41(17Q11.2) WILD-TYPE 305  16  10  30
D91V4, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  R0                           66                            305
  R1                            6                             16
  R2                            6                             10
  RX                           10                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(92) Variable = DEL PEAK 42(17Q21.31) MUTATION ANALYSIS
D92V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 42(17Q21.31) MUTATED    80  33
  DEL PEAK 42(17Q21.31) WILD-TYPE 367  57
  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                            113                             424 
  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                             33                              57 
$`DEL PEAK 42(17Q21.31) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D 
       41.06        29.39        20.81        10.19       110.63        57.80 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       36.39        61.18         1.38        27.09        22.06        66.41 
TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C 
       33.30        10.19        17.92        36.00        23.74        39.52 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A3LO 
       65.75        60.53        17.59        31.99       118.19        25.51 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BI TCGA-AJ-A3EM 
       18.41        20.25        14.43        21.14        18.90        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H 
       17.06        21.21        16.87        21.99        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX 
       36.89        48.79       125.42        97.71        46.78        36.13 
TCGA-AW-A1PO TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2IO 
        0.56        34.65        25.51        30.12        71.24        64.93 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0K3 
        0.56        43.82         0.20        20.52         0.30        27.29 
TCGA-B5-A0K8 TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
       27.85        61.68       102.31       136.60        39.35        29.65 
TCGA-B5-A5OD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD 
       34.13        15.45        22.39        35.08        24.13        16.64 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
       92.88        83.64        29.95        22.55        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 
       31.07        14.73        28.08        13.22        18.25         2.07 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NO 
       18.84        17.29        71.61       109.08        25.91         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       12.39        31.10        49.15        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GR 
       34.39        22.26        16.34        54.15        23.90        17.62 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 
       11.08        12.59        29.10        11.38        68.38        77.33 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W0 
       96.69        28.93        30.67         1.74        17.75        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A8F1 
       26.10        18.21        38.70        22.59         4.44 

$`DEL PEAK 42(17Q21.31) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AP-A0LF 
       88.18        60.53        30.15        16.83        18.08        93.99 
TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CR TCGA-AX-A2HF TCGA-B5-A0JN 
       95.47        67.66        12.26        23.05        27.88        80.38 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        16.93         6.21        22.78        17.88 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 
       14.40        18.87        19.89         5.88        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       73.32         0.43        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       74.10        46.55        73.87        36.82        28.27        54.02 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        37.91        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 
       42.35        15.95        31.99        36.33        33.07        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-AJ-A23O 
       28.64        24.72        34.95        14.96        11.21        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK 
       19.79        35.15        34.36        34.16        18.12        33.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
        1.64        14.66        22.49        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       20.78         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       86.07        48.03        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        61.08        35.74        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        77.39        13.28        32.91        26.37        32.02 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       25.91        34.09        76.83        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58         4.77        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       38.24        17.75        30.74         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O 
      113.36        88.34        75.72        54.44        73.64        85.78 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       52.04        32.09        77.23        73.28        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       225.50        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       51.45        14.70        48.43        11.87        52.54        31.36 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        93.50        71.84        27.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       14.83        13.78        14.73        14.01        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       35.90        31.00        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
      114.90        85.84        82.39        81.57        72.72        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        89.59        63.58        86.99        66.48        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
        8.55         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        0.72        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN 
       48.79         8.48        58.95        15.88         4.27         2.20 
TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
      100.83        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30        35.38       110.10        23.38        79.10 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        50.73        35.15        38.07        27.16        46.42 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       26.96        38.47        51.09        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       18.84        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       19.33        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 
       32.52        14.14        14.70        16.96        39.88         7.99 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       25.22        59.01         9.34        59.28        41.56        78.38 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
       14.04         9.47        23.24        21.30         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                          136.6                           225.5 
  DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE 
                          27.29                           30.74 
[1] "0.2 - 136.6 (27.3)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.3"
D92V2, binary
                                 cls
clus                                0   1
  DEL PEAK 42(17Q21.31) MUTATED    56  49
  DEL PEAK 42(17Q21.31) WILD-TYPE 234 175
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(17Q21.31) MUTATED     56   49
  DEL PEAK 42(17Q21.31) WILD-TYPE  234  175
     clus
vv    DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE
  NO                             56                             234
  YES                            49                             175
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 42(17Q21.31) MUTATED                                        47
  DEL PEAK 42(17Q21.31) WILD-TYPE                                     357
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 42(17Q21.31) MUTATED                               6
  DEL PEAK 42(17Q21.31) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 42(17Q21.31) MUTATED                                  61
  DEL PEAK 42(17Q21.31) WILD-TYPE                                52
D92V3, multiclass
                                         clus
vv                                        DEL PEAK 42(17Q21.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            47
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  61
                                         clus
vv                                        DEL PEAK 42(17Q21.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             357
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 42(17Q21.31) MUTATED    68   6   6  14
  DEL PEAK 42(17Q21.31) WILD-TYPE 303  16  10  26
D92V4, multiclass
    clus
vv   DEL PEAK 42(17Q21.31) MUTATED DEL PEAK 42(17Q21.31) WILD-TYPE
  R0                            68                             303
  R1                             6                              16
  R2                             6                              10
  RX                            14                              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(93) Variable = DEL PEAK 43(18Q21.2) MUTATION ANALYSIS
D93V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(18Q21.2) MUTATED    69  20
  DEL PEAK 43(18Q21.2) WILD-TYPE 378  70
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                            89                            448 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                            20                             70 
$`DEL PEAK 43(18Q21.2) MUTATED`
TCGA-AJ-A2QM TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-D1-A3JP 
       29.39        93.99        23.05         1.38        80.38        16.93 
TCGA-EY-A214 TCGA-EY-A547 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0G5 
       14.40        17.92         5.88        36.00        23.74        37.02 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K3 
       65.75        60.53        36.82        17.59        31.99        66.15 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A3BD 
       28.64        25.51        14.96        20.25        21.14        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3NF TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI 
       18.12        21.21        45.53       125.42        36.36        97.71 
TCGA-AX-A0IU TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3FZ 
       35.74        32.02        76.83         4.77         2.96         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A11H TCGA-B5-A11P 
       20.52         0.30         0.30         0.39        88.34        52.04 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE 
       31.36       136.60        39.35        34.95        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP 
       22.39        35.08        16.64        92.88        83.64        29.95 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 
       37.32        18.67         3.95        28.08         0.72         2.07 
TCGA-D1-A3DH TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       18.84       109.08        25.91        31.10       110.10        79.10 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GO 
       49.15        37.71        51.42        27.16        54.15        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3QX 
       18.84        22.03        11.08        20.05        45.76        32.52 
TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W0 
       68.38         9.34        28.93        78.38        14.04        13.28 
TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
        9.47        23.24        38.70         4.44         0.07 

$`DEL PEAK 43(18Q21.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG 
       41.06        88.18        60.53        30.15        16.83        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B 
       20.81        10.19       110.63        57.80        95.47        67.66 
TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M6 
       12.26        36.39        61.18        27.88        27.09        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       66.41        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       17.88        10.19        18.87        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       74.10        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        37.91        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 
       15.95        31.99        36.33        33.07       118.19        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       34.95        11.21        18.41        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       35.15        34.36        18.90        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        22.26        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 
       12.82        20.78         2.70        35.11         0.13       129.80 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
       21.99        23.31        86.07        48.03        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       66.25        46.72        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       61.64        80.78        49.22        25.08        71.67        90.97 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       60.23        45.86        27.85        51.12        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        30.02        60.66        61.08        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        77.39        13.28        32.91        34.65        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       26.37        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       37.58        30.12        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        38.24        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3G8 
        0.23         0.20         0.56        43.82         0.26         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J 
       13.45        59.84       185.79       113.36        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       73.64        61.68        85.78        32.09        77.23        73.28 
TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       16.73        19.56        19.50        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      225.50       102.31        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       11.87        52.54        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.01        15.45         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        35.90        31.00        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       85.55        78.21         4.80        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       86.99        66.48        16.83         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JQ 
       48.79         8.48        58.95        15.88         4.27        17.29 
TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        2.20        71.61       100.83        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       12.39        23.38        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        10.92        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        38.07        46.42        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GR 
       23.34        23.34        23.90        33.34        32.71        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        32.78        15.81        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 
       22.82        31.04        29.10        27.35        11.38        14.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.70        16.96        39.88        77.33         7.99        25.22 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       96.69        59.01        30.67        59.28        41.56         1.74 
TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
       17.75        26.10        18.21        21.30        22.59         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        20.75        18.28         0.23 

  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE 
                        28.080                         30.135 
[1] "0.1 - 136.6 (28.1)" "0.1 - 225.5 (30.1)"
[1] "hr=" "1.5"
D93V2, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q21.2) MUTATED    48  33
  DEL PEAK 43(18Q21.2) WILD-TYPE 242 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q21.2) MUTATED     48   33
  DEL PEAK 43(18Q21.2) WILD-TYPE  242  191
     clus
vv    DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  NO                            48                            242
  YES                           33                            191
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 43(18Q21.2) MUTATED                                        38
  DEL PEAK 43(18Q21.2) WILD-TYPE                                     366
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 43(18Q21.2) MUTATED                               6
  DEL PEAK 43(18Q21.2) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 43(18Q21.2) MUTATED                                  46
  DEL PEAK 43(18Q21.2) WILD-TYPE                                67
D93V3, multiclass
                                         clus
vv                                        DEL PEAK 43(18Q21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           38
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 46
                                         clus
vv                                        DEL PEAK 43(18Q21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            366
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(18Q21.2) MUTATED    50   5   5  10
  DEL PEAK 43(18Q21.2) WILD-TYPE 321  17  11  30
D93V4, multiclass
    clus
vv   DEL PEAK 43(18Q21.2) MUTATED DEL PEAK 43(18Q21.2) WILD-TYPE
  R0                           50                            321
  R1                            5                             17
  R2                            5                             11
  RX                           10                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(94) Variable = DEL PEAK 44(18Q23) MUTATION ANALYSIS
D94V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 44(18Q23) MUTATED    71  26
  DEL PEAK 44(18Q23) WILD-TYPE 376  64
  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                          97                          440 
  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                          26                           64 
$`DEL PEAK 44(18Q23) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AP-A0LF TCGA-AX-A1CR TCGA-AX-A3G3 TCGA-B5-A0JN 
       41.06        20.81        93.99        23.05         1.38        80.38 
TCGA-D1-A3JP TCGA-EY-A212 TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0G5 
       16.93        10.19         5.88        36.00        23.74        37.02 
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG 
       65.75        60.53        36.82        37.91        17.59        31.99 
TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       36.33        66.15        28.64        25.51        14.96        20.25 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3NF TCGA-AJ-A3TW 
       14.43        21.14        34.16        18.12        21.21        16.87 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A0IU TCGA-AX-A1CA 
       21.99        45.53        36.36        97.71        35.74        32.02 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        4.77        30.12         2.96         0.20        20.52         0.30 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JX TCGA-B5-A11E TCGA-B5-A11P TCGA-B5-A1MY 
        0.30         0.39        58.75        59.84        52.04        11.87 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP 
      136.60        39.35        34.95        15.45        23.70        22.39 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       35.08        31.00        16.64        61.87        92.88        83.64 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 
       37.32        18.67         3.95        28.08         0.72         2.07 
TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A2QT TCGA-DI-A2QU 
       18.84        17.29       109.08        25.91        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ 
      110.10        79.10        49.15        37.71        51.42        27.16 
TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OO 
       54.15        18.84        22.03        11.08        20.05        45.76 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       29.10        32.52        68.38        59.01         9.34        28.93 
TCGA-FI-A2F8 TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-QS-A8F1 
       30.67        14.04        13.28         9.47        38.70         4.44 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 44(18Q23) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       10.19       110.63        57.80        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       36.39        61.18        27.88        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       14.40        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       73.32         0.43        39.52        10.29       106.88       149.56 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       74.10        46.55        73.87        28.27        54.02        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ 
       31.99        33.07       118.19        24.72        34.95        11.21 
TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI 
       18.41        10.26        19.79        35.15        34.36        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       33.90         1.64        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13       129.80        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.62        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      117.99       110.37        66.25        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       34.65        25.51        26.37        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 
       85.48        73.41        80.25        37.58        71.24        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.26         1.18        18.35        14.47        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       55.30        59.24        86.01        69.27        71.44        48.59 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       36.49        72.62        27.29        57.76        64.21        63.55 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       27.85        13.45       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       16.57       225.50       102.31        50.89        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       48.43        52.54        31.36        96.30        93.50        71.84 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       27.65        29.65        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        71.24        63.68        74.63 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       10.72        41.52        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       59.74        21.17        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.73        14.01        15.45         9.57        20.02        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       11.31        35.90        34.98        35.90        31.76        24.99 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
       24.13        13.18        10.03         9.86        46.95        24.33 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        97.41       114.90        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI 
       72.72        73.25        59.51        89.59        63.58        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        0.69         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KN 
       48.79         8.48        58.95        15.88         4.27         2.20 
TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
       71.61       100.83        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX 
       39.29        36.62        24.30        35.38         9.37        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       58.95         2.37        45.57        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       46.42        26.96        22.26        16.34        38.47        51.09 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GT 
       23.90        33.34        32.71        19.27        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM 
       32.78        15.81        37.05        19.33        12.59        22.82 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        27.35        11.38        14.14        14.70        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F9 
       39.88        77.33         7.99        25.22        96.69        59.28 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 
       41.56        78.38         1.74        17.75        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        21.30        22.59         8.19        17.16         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       22.65        39.95        24.95        23.64        14.83        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                        0.07                         0.13 
  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                       136.6                        225.5 
  DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE 
                      28.080                       30.115 
[1] "0.1 - 136.6 (28.1)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.1"
D94V2, binary
                              cls
clus                             0   1
  DEL PEAK 44(18Q23) MUTATED    55  33
  DEL PEAK 44(18Q23) WILD-TYPE 235 191
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 44(18Q23) MUTATED     55   33
  DEL PEAK 44(18Q23) WILD-TYPE  235  191
     clus
vv    DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE
  NO                          55                          235
  YES                         33                          191
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 44(18Q23) MUTATED                                        39
  DEL PEAK 44(18Q23) WILD-TYPE                                     365
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 44(18Q23) MUTATED                               6
  DEL PEAK 44(18Q23) WILD-TYPE                            16
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 44(18Q23) MUTATED                                  53
  DEL PEAK 44(18Q23) WILD-TYPE                                60
D94V3, multiclass
                                         clus
vv                                        DEL PEAK 44(18Q23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         39
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               53
                                         clus
vv                                        DEL PEAK 44(18Q23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          365
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 44(18Q23) MUTATED    57   5   8   9
  DEL PEAK 44(18Q23) WILD-TYPE 314  17   8  31
D94V4, multiclass
    clus
vv   DEL PEAK 44(18Q23) MUTATED DEL PEAK 44(18Q23) WILD-TYPE
  R0                         57                          314
  R1                          5                           17
  R2                          8                            8
  RX                          9                           31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(95) Variable = DEL PEAK 45(19P13.3) MUTATION ANALYSIS
D95V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(19P13.3) MUTATED   110  46
  DEL PEAK 45(19P13.3) WILD-TYPE 337  44
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                           156                            381 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                            46                             44 
$`DEL PEAK 45(19P13.3) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AJ-A3IA TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       41.06        29.39        20.81       110.63        57.80        93.99 
TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       67.66        36.39        23.05        61.18        27.88         1.38 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-D1-A3JP 
       80.38        27.09        22.06        66.41        12.56        16.93 
TCGA-EY-A212 TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0G5 
       10.19        14.40        36.00        23.74        39.52        37.02 
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 
       60.53        37.91        31.99        36.33       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N 
       28.64        25.51        14.96        18.41        20.25        14.43 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF 
       21.14        34.16        18.12         1.64        22.26        21.21 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H 
       16.87        16.87        20.78        21.99        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       36.89        48.79       125.42        97.71        46.78        21.90 
TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       36.13        35.74        37.78        34.65        25.51        32.02 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A2IO 
       76.83         4.77        30.12        71.24         2.96        64.93 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
        0.39        27.29        27.85        75.72        52.04       102.31 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
       50.89        11.87        31.36       136.60        39.35        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0MT TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC 
       34.13        34.95        21.17        15.45        22.39        35.08 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V 
       24.13        92.88        83.64        29.95        22.55        39.48 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU 
       11.51        31.07        18.67        14.73        28.08        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3JQ 
        0.72        18.25         2.07        58.95         4.27        17.29 
TCGA-DF-A2KS TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
      109.08        35.38         9.37        12.39        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU 
       79.10        10.92        37.71        51.42        19.40        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR 
       16.34        54.15        23.90        32.71        18.84        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.03        15.81        11.08        20.05        27.35        32.52 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       11.38        14.70        68.38        77.33        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.34        28.93        30.67        59.28        41.56        78.38 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74        17.75        14.04        13.28         9.47        26.10 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.24        38.70        22.59         8.19         4.44         0.07 

$`DEL PEAK 45(19P13.3) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3NH 
       88.18        60.53        30.15        16.83        18.08        10.19 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 
       95.47        12.26        61.87        51.55        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       17.88        18.87        17.92        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       13.84        73.32         0.43        10.29       106.88       149.56 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37       123.68 
TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       74.10        65.75        46.55        73.87        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K5 
       29.06        42.35        15.95        31.99        33.07        24.72 
TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       34.95        11.21        10.26        19.79        35.15        34.36 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
       18.90        33.90        14.66        22.49        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       20.65        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       12.82         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       86.07        48.03        23.87        12.62        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        66.25        36.36        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        90.97        55.89        31.30        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO 
        6.71        60.23        45.86        27.85        51.12         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       13.28        32.91        26.37        25.91        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       73.41        80.25        37.58        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        38.24        17.75        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         0.56         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       71.44        48.59        36.49        72.62        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       63.55        13.45        59.84       185.79       113.36        88.34 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       225.50        51.45        14.70        48.43        52.54 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       96.30        93.50        71.84        27.65        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       43.04        59.74        20.28        15.42        51.06        52.01 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       34.29        52.64        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45         9.57        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98        35.90        31.00 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       31.76        24.99        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       89.59        63.58        86.99        66.48        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A3DA 
       15.06         1.05         3.95        48.79         8.48        15.88 
TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       18.84         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       27.16        25.91        16.31        39.29        36.62        24.30 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        58.95         2.37        45.57        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        49.15        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        46.42        26.96        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL 
       53.88        24.36        27.16        23.34        23.34        33.34 
TCGA-EY-A1GO TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       19.27        16.11        32.78        37.05        19.33        12.59 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A5W2 
       22.82        45.76        31.04        29.10        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 
       39.88         7.99        25.22        18.21        21.30        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE 
                         27.60                          30.74 
[1] "0.1 - 136.6 (27.6)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.8"
D95V2, binary
                                cls
clus                               0   1
  DEL PEAK 45(19P13.3) MUTATED    78  66
  DEL PEAK 45(19P13.3) WILD-TYPE 212 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(19P13.3) MUTATED     78   66
  DEL PEAK 45(19P13.3) WILD-TYPE  212  158
     clus
vv    DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  NO                            78                            212
  YES                           66                            158
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 45(19P13.3) MUTATED                                        45
  DEL PEAK 45(19P13.3) WILD-TYPE                                     359
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 45(19P13.3) MUTATED                              10
  DEL PEAK 45(19P13.3) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 45(19P13.3) MUTATED                                 102
  DEL PEAK 45(19P13.3) WILD-TYPE                                11
D95V3, multiclass
                                         clus
vv                                        DEL PEAK 45(19P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           45
  MIXED SEROUS AND ENDOMETRIOID                                     10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                102
                                         clus
vv                                        DEL PEAK 45(19P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            359
  MIXED SEROUS AND ENDOMETRIOID                                       12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(19P13.3) MUTATED    94   9  10  15
  DEL PEAK 45(19P13.3) WILD-TYPE 277  13   6  25
D95V4, multiclass
    clus
vv   DEL PEAK 45(19P13.3) MUTATED DEL PEAK 45(19P13.3) WILD-TYPE
  R0                           94                            277
  R1                            9                             13
  R2                           10                              6
  RX                           15                             25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(96) Variable = DEL PEAK 46(19P12) MUTATION ANALYSIS
D96V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 46(19P12) MUTATED    44  14
  DEL PEAK 46(19P12) WILD-TYPE 403  76
  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                          58                          479 
  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                          14                           76 
$`DEL PEAK 46(19P12) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A2QM TCGA-AP-A05D TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0YV 
       41.06        29.39        57.80        80.38        22.06        12.56 
TCGA-D1-A3JP TCGA-EY-A214 TCGA-EY-A72D TCGA-KP-A3VZ TCGA-A5-A0GN TCGA-A5-A3LO 
       16.93        14.40         5.88        23.74        60.53        25.51 
TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A3K1 TCGA-AP-A5FX 
       34.16         1.64        21.21        16.87        21.90        36.13 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK 
       34.65        32.02        76.83         4.77        71.24         2.96 
TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JZ TCGA-B5-A11P TCGA-B5-A1MS 
        0.20         0.30         0.39        71.44        52.04       102.31 
TCGA-B5-A1MU TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A18C 
       50.89       136.60        39.35        34.13        34.95        15.45 
TCGA-BG-A3PP TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16N TCGA-DF-A2KR TCGA-DI-A2QT 
       22.39        61.87        92.88        31.07        71.61        12.39 
TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2OQ 
       49.15        51.42        26.96        15.81        11.08        29.10 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       11.38        14.70        68.38        77.33         9.34        28.93 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
        9.47        26.10        38.70        22.59 

$`DEL PEAK 46(19P12) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A3BG TCGA-AJ-A3IA 
       88.18        60.53        30.15        16.83        18.08        20.81 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       10.19       110.63        93.99        95.47        67.66        12.26 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB 
       36.39        23.05        61.18        27.88         1.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       66.41        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        33.30         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2CX TCGA-FI-A2D5 
       10.19        18.87        17.92        19.89        66.77        13.84 
TCGA-FI-A2F4 TCGA-KJ-A3U4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       73.32        36.00         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ 
      105.37       123.68        74.10        65.75        46.55        73.87 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        54.02        23.21        68.65        37.91 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 
       31.99        31.99        36.33        33.07       118.19        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK 
       28.64        24.72        34.95        14.96        11.21        18.41 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       20.25        14.43        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        18.12        18.90        33.90        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.26        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.70        35.11         0.13       129.80        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07        48.03        63.91        45.53        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       26.37        25.91        34.09        85.48        73.41        80.25 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       37.58        30.12        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       38.24        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.20         0.56        43.82        20.52         0.30         0.26 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        86.37        55.30 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K1 
       59.24        86.01        58.75        69.27        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       72.62        27.29        57.76        64.21        63.55        27.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       13.45        59.84       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        73.64        61.68        85.78        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
       16.57       225.50        51.45        14.70        48.43        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       52.54        31.36        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       29.65        41.06        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        71.24        63.68        74.63        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT 
       48.56        23.47        43.30        43.04        59.74        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        51.06        52.01        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        14.83        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45         9.57        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98        35.90        35.08        31.00        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        30.74        97.41       114.90        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       82.39        81.57        72.72        73.25        59.51        89.59 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP 
       63.58        83.64        86.99        66.48        16.83        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
        8.55         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KS TCGA-DF-A2KU 
        4.27        18.84        17.29         2.20       109.08       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 TCGA-DI-A0WH TCGA-DI-A1BU 
       89.33        10.92        27.16        25.91        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30        35.38         9.37        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        79.10        58.95         2.37        45.57        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       50.73        35.15        38.07        27.16        46.42        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       16.34        38.47        51.09        14.99        54.15        53.88 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        23.90        33.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       32.71        19.27        18.84        17.62        22.03        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON 
       32.78        37.05        19.33        12.59        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A5W2 
       45.76        31.04        27.35        32.52        14.14        16.96 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F8 
       39.88         7.99        25.22        96.69        59.01        30.67 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       59.28        41.56        78.38         1.74        17.75        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
       13.28        18.21        23.24        21.30         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        20.75        18.28         0.07         0.23 

  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                        0.20                         0.07 
  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                       136.6                        225.5 
  DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE 
                      29.015                       30.020 
[1] "0.2 - 136.6 (29.0)" "0.1 - 225.5 (30.0)"
[1] "hr=" "1.6"
D96V2, binary
                              cls
clus                             0   1
  DEL PEAK 46(19P12) MUTATED    25  28
  DEL PEAK 46(19P12) WILD-TYPE 265 196
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 46(19P12) MUTATED     25   28
  DEL PEAK 46(19P12) WILD-TYPE  265  196
     clus
vv    DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE
  NO                          25                          265
  YES                         28                          196
[1] 2 2
[1] FALSE
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 46(19P12) MUTATED                                        21
  DEL PEAK 46(19P12) WILD-TYPE                                     383
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 46(19P12) MUTATED                               5
  DEL PEAK 46(19P12) WILD-TYPE                            17
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 46(19P12) MUTATED                                  32
  DEL PEAK 46(19P12) WILD-TYPE                                81
D96V3, multiclass
                                         clus
vv                                        DEL PEAK 46(19P12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         21
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               32
                                         clus
vv                                        DEL PEAK 46(19P12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          383
  MIXED SEROUS AND ENDOMETRIOID                                     17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 46(19P12) MUTATED    33   3   2   8
  DEL PEAK 46(19P12) WILD-TYPE 338  19  14  32
D96V4, multiclass
    clus
vv   DEL PEAK 46(19P12) MUTATED DEL PEAK 46(19P12) WILD-TYPE
  R0                         33                          338
  R1                          3                           19
  R2                          2                           14
  RX                          8                           32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(97) Variable = DEL PEAK 47(19Q13.43) MUTATION ANALYSIS
D97V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 47(19Q13.43) MUTATED    47  19
  DEL PEAK 47(19Q13.43) WILD-TYPE 400  71
  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                             66                             471 
  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                             19                              71 
$`DEL PEAK 47(19Q13.43) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AP-A05D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A3G3 
       41.06        20.81        57.80        36.39        23.05         1.38 
TCGA-EY-A214 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN 
       14.40        36.00        23.74        39.52        65.75        60.53 
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       37.91       118.19        28.64        25.51        20.25        14.43 
TCGA-AJ-A3BI TCGA-AJ-A3NF TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H 
       18.90        21.21        20.78        21.99        63.91        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AX-A0IW TCGA-AX-A1C8 
       48.79       125.42        36.36        21.90        37.78        25.51 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G4 
       76.83         4.77        71.24         2.96         0.20         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
        0.26         0.30        52.04       102.31        50.89        11.87 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-D1-A16G TCGA-D1-A16I 
       34.95        15.45        22.39        35.08        27.42        11.51 
TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GW 
        4.27        17.29        71.61        22.26        23.90        11.08 
TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2EW 
       12.59        29.10        27.35        32.52        68.38        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
        9.34        30.67        26.10        38.70         4.44         0.07 

$`DEL PEAK 47(19Q13.43) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06B TCGA-AX-A06D 
       10.19       110.63        93.99        95.47        67.66        12.26 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M6 TCGA-BG-A0M8 
       61.18        27.88        80.38        27.09        22.06        66.41 
TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       61.87        51.55        12.56        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK 
        4.44        47.84        16.93        33.30         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       17.88        10.19        18.87        17.92        19.89         5.88 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 
       66.77        13.84        73.32         0.43        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      105.37       123.68        74.10        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       36.33        33.07        66.15        24.72        34.95        14.96 
TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       11.21        18.41        10.26        21.14        19.79        35.15 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36        34.16        18.12        33.90         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        22.26        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       12.82         2.70        35.11         0.13       129.80        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07        48.03        36.89        23.87        12.62        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        66.25        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        49.15         6.71        60.23        45.86        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       51.12        36.13         0.56        13.58        33.21        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       80.55        88.24        71.51        35.34        45.99        79.46 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       49.87        57.47        27.39        30.02        60.66        61.08 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.74        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       34.65        26.37        32.02        25.91        34.09        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       73.41        80.25        37.58        30.12        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        38.24        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       64.93         0.23         0.20         0.56        43.82        20.52 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47         0.39        56.91        86.37 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       55.30        59.24        86.01        58.75        69.27        71.44 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       48.59        36.49        72.62        27.29        57.76        64.21 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       63.55        27.85        13.45        59.84       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW 
       18.41        17.36        16.57       225.50        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       48.43        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       71.84        39.35        27.65        29.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        59.74        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       51.06        52.01        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 
       14.83        13.78        14.73        14.01        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.90        31.00        31.76        24.99        24.13        16.64 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.36        37.51        36.79        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KN 
       48.79         8.48        58.95        15.88        18.84         2.20 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        23.38        79.10        58.95 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        45.57        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       57.60        51.52        51.42        19.40        34.39        50.73 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       35.15        38.07        27.16        46.42        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       37.05        19.33        22.82        20.05        45.76        31.04 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 
       11.38        14.14        14.70        16.96        39.88        77.33 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV 
        7.99        25.22        96.69        28.93        59.28        41.56 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 
       78.38         1.74        17.75        14.04        13.28         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       18.21        23.24        21.30        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       20.75        18.28         0.23 

  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                           0.07                            0.13 
  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                         125.42                          225.50 
  DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE 
                         25.805                          30.150 
[1] "0.1 - 125.4 (25.8)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.1"
D97V2, binary
                                 cls
clus                                0   1
  DEL PEAK 47(19Q13.43) MUTATED    35  24
  DEL PEAK 47(19Q13.43) WILD-TYPE 255 200
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 47(19Q13.43) MUTATED     35   24
  DEL PEAK 47(19Q13.43) WILD-TYPE  255  200
     clus
vv    DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE
  NO                             35                             255
  YES                            24                             200
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 47(19Q13.43) MUTATED                                        20
  DEL PEAK 47(19Q13.43) WILD-TYPE                                     384
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 47(19Q13.43) MUTATED                               4
  DEL PEAK 47(19Q13.43) WILD-TYPE                            18
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 47(19Q13.43) MUTATED                                  43
  DEL PEAK 47(19Q13.43) WILD-TYPE                                70
D97V3, multiclass
                                         clus
vv                                        DEL PEAK 47(19Q13.43) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            20
  MIXED SEROUS AND ENDOMETRIOID                                       4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  43
                                         clus
vv                                        DEL PEAK 47(19Q13.43) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             384
  MIXED SEROUS AND ENDOMETRIOID                                        18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 47(19Q13.43) MUTATED    37   6   3   8
  DEL PEAK 47(19Q13.43) WILD-TYPE 334  16  13  32
D97V4, multiclass
    clus
vv   DEL PEAK 47(19Q13.43) MUTATED DEL PEAK 47(19Q13.43) WILD-TYPE
  R0                            37                             334
  R1                             6                              16
  R2                             3                              13
  RX                             8                              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(98) Variable = DEL PEAK 48(20P12.1) MUTATION ANALYSIS
D98V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 48(20P12.1) MUTATED    21  14
  DEL PEAK 48(20P12.1) WILD-TYPE 426  76
  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                            35                            502 
  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                            14                             76 
$`DEL PEAK 48(20P12.1) MUTATED`
TCGA-2E-A9G8 TCGA-BG-A0M6 TCGA-D1-A3JP TCGA-EY-A547 TCGA-A5-A0G2 TCGA-A5-A0GN 
       41.06        22.06        16.93        17.92       149.56        60.53 
TCGA-A5-A0R6 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AP-A05H TCGA-AP-A3K1 TCGA-AX-A1CF 
       37.91        20.25        34.16        45.53        21.90        76.83 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0K8 TCGA-B5-A1MS 
        4.77        40.80        20.52         0.30        27.85       102.31 
TCGA-B5-A3FH TCGA-B5-A5OE TCGA-BG-A0MG TCGA-BG-A0MO TCGA-BG-A18C TCGA-BK-A4ZD 
       27.65        34.95        48.56        43.04        15.45        16.64 
TCGA-D1-A161 TCGA-D1-A17M TCGA-D1-A3JQ TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EY-A1GW 
       29.33        10.22        17.29         9.37        12.39        11.08 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-QS-A8F1 
       29.10        11.38        77.33        41.56         4.44 

$`DEL PEAK 48(20P12.1) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A0LS 
       20.81        10.19       110.63        57.80        93.99        95.47 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       67.66        12.26        36.39        23.05        61.18        27.88 
TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
        1.38        80.38        27.09        66.41        61.87        51.55 
TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       12.56        14.27         1.81        19.79         4.44        47.84 
TCGA-E6-A8L9 TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A214 
       33.30         6.21        22.78        17.88        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 
       18.87        19.89         5.88        66.77        13.84        73.32 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       36.00        23.74         0.43        39.52        10.29       106.88 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
      123.68        74.10        65.75        46.55        73.87        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        54.02        23.21        68.65        17.59        19.59 
TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG 
       24.62        29.06        42.35        15.95        31.99        31.99 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33        33.07       118.19        66.15        28.64        24.72 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-A5-A7WJ TCGA-A5-A7WK TCGA-AJ-A23N 
       34.95        25.51        14.96        11.21        18.41        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        21.14        19.79        35.15        34.36        18.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90        33.90         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       20.78         2.70        35.11         0.13       129.80        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07        48.03        63.91        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.62        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       66.25        36.36        97.71        46.72        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        33.40        61.64        80.78        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        90.97        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       57.47        27.39        30.02        60.66        61.08        35.74 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        77.39        13.28        32.91 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       34.65        25.51        26.37        32.02        25.91        34.09 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H5 
       85.48        73.41        80.25        37.58        30.12        71.24 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        38.24        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       43.82         0.20         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        86.37        55.30        59.24 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       86.01        58.75        69.27        71.44        48.59        36.49 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       72.62        27.29        57.76        64.21        63.55        13.45 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
       59.84       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       73.64        61.68        85.78        52.04        32.09        77.23 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       73.28        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       225.50        50.89        51.45        14.70        48.43 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        52.54        31.36       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       71.84        39.35        29.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MQ 
       74.63        10.72        41.52        23.47        43.30        59.74 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        51.06        52.01        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        14.83        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45         9.57        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31        22.39        35.90        34.98        35.90        35.08 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       31.00        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE 
        9.86        46.95        24.33        85.55        78.21         4.80 
TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 
       77.95        61.87        67.99        96.49        30.74        97.41 
TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       92.88       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93        22.55         1.74        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A163 TCGA-D1-A165 
       30.08        29.88         1.91         3.68        32.58         0.66 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95        48.79         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR 
       58.95        15.88         4.27        18.84         2.20        71.61 
TCGA-DF-A2KS TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DF-A2L0 
      109.08       100.83        89.33        10.92        27.16        25.91 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        35.38        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        46.42        26.96        22.26        16.34        38.47 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       51.09        14.99        54.15        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        23.90        33.34        32.71        19.27 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.62        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       37.05        19.33        12.59        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        27.35        32.52        14.14        14.70        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       68.38        39.88         7.99        25.22        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
        9.34        28.93        30.67        59.28        78.38         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       17.75        14.04        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       23.24        21.30        38.70        22.59         8.19        17.16 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        22.65        39.95        24.95        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       20.75        18.28         0.07         0.23 

  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                          0.30                           0.07 
  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                        149.56                         225.50 
  DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE 
                         27.65                          30.10 
[1] "0.3 - 149.6 (27.6)" "0.1 - 225.5 (30.1)"
[1] "hr=" "2.9"
D98V2, binary
                                cls
clus                               0   1
  DEL PEAK 48(20P12.1) MUTATED    17  15
  DEL PEAK 48(20P12.1) WILD-TYPE 273 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 48(20P12.1) MUTATED     17   15
  DEL PEAK 48(20P12.1) WILD-TYPE  273  209
     clus
vv    DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE
  NO                            17                            273
  YES                           15                            209
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 48(20P12.1) MUTATED                                        16
  DEL PEAK 48(20P12.1) WILD-TYPE                                     388
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 48(20P12.1) MUTATED                               1
  DEL PEAK 48(20P12.1) WILD-TYPE                            21
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 48(20P12.1) MUTATED                                  18
  DEL PEAK 48(20P12.1) WILD-TYPE                                95
D98V3, multiclass
                                         clus
vv                                        DEL PEAK 48(20P12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           16
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 18
                                         clus
vv                                        DEL PEAK 48(20P12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            388
  MIXED SEROUS AND ENDOMETRIOID                                       21
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 48(20P12.1) MUTATED    20   1   2   5
  DEL PEAK 48(20P12.1) WILD-TYPE 351  21  14  35
D98V4, multiclass
    clus
vv   DEL PEAK 48(20P12.1) MUTATED DEL PEAK 48(20P12.1) WILD-TYPE
  R0                           20                            351
  R1                            1                             21
  R2                            2                             14
  RX                            5                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(99) Variable = DEL PEAK 49(22Q12.1) MUTATION ANALYSIS
D99V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 49(22Q12.1) MUTATED    68  26
  DEL PEAK 49(22Q12.1) WILD-TYPE 379  64
  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                            94                            443 
  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                            26                             64 
$`DEL PEAK 49(22Q12.1) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CP 
       41.06        20.81        10.19        57.80        67.66        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB TCGA-BG-A0M8 TCGA-E6-A8L9 
       61.18        27.88         1.38        27.09        66.41        33.30 
TCGA-EY-A214 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN 
       14.40        17.92        36.00        23.74        65.75        60.53 
TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23N 
       36.82        17.59        31.99        36.33        25.51        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 
       21.14        19.79        18.12        18.90         1.64        17.06 
TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IU 
       16.87        45.53        48.79        46.78        36.13        35.74 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A2H4 TCGA-AX-A2H5 
       37.78        34.65        25.51        32.02        30.12        71.24 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
       30.74         2.96        43.82        20.52         0.30         0.26 
TCGA-AX-A3G7 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 
        0.30        75.72        52.04       102.31        31.36       136.60 
TCGA-B5-A3FD TCGA-BG-A0MT TCGA-BG-A0VZ TCGA-BG-A18C TCGA-BG-A2AD TCGA-BK-A0CC 
       39.35        21.17        52.64        15.45        20.02        35.08 
TCGA-BK-A139 TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       31.00        92.88        22.55        31.07        18.67         3.95 
TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-DF-A2KR TCGA-DF-A2KS 
       28.08         0.72         2.07         4.27        71.61       109.08 
TCGA-DF-A2L0 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A3AZ 
       25.91        12.39        31.10       110.10        49.15        27.16 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW 
       16.34        54.15        32.71        18.84        17.62        11.08 
TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-FI-A3PX TCGA-H5-A2HR 
       12.59        45.76        29.10        77.33        78.38         1.74 
TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A914 TCGA-SL-A6J9 
       14.04        26.10        22.59         0.07 

$`DEL PEAK 49(22Q12.1) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A053 TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CR TCGA-B5-A0JN 
      110.63        93.99        95.47        12.26        23.05        80.38 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BG-A220 TCGA-BG-A221 
       22.06        61.87        51.55        12.56        14.27         1.81 
TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK 
       19.79         4.44        47.84        16.93         6.21        22.78 
TCGA-EY-A1GQ TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       17.88        10.19        18.87        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 
       13.84        73.32         0.43        39.52        10.29       106.88 
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
      149.56        37.02        83.51        17.85        32.78       112.54 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
      105.37       123.68        74.10        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       54.02        23.21        68.65        37.91        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A2K2 
       29.06        42.35        15.95        31.99        33.07       118.19 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-A5-A7WJ 
       66.15        28.64        24.72        34.95        14.96        11.21 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       18.41        20.25        10.26        35.15        34.36        34.16 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NE 
       33.90        14.66        22.49        22.26        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89        23.87        12.62        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        66.25        36.36        97.71        46.72        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT 
       27.12        82.52        33.40        61.64        80.78        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        90.97        55.89        31.30        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        60.23        45.86        27.85        51.12 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90         0.56        13.58        33.21        29.69        80.55 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       88.24        71.51        35.34        45.99        79.46        49.87 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       57.47        27.39        30.02        60.66        61.08        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC 
       40.11        77.39        13.28        32.91        26.37        25.91 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       34.09        76.83        85.48        73.41        80.25        37.58 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
        4.77        40.80        81.37        34.32        46.49        38.24 
TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       17.75        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.20         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       86.37        55.30        59.24        86.01        58.75        69.27 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       71.44        48.59        36.49        72.62        27.29        57.76 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       64.21        63.55        27.85        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50        50.89        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        11.87        52.54        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       71.84        27.65        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        71.24 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       63.68        74.63        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.30        43.04        59.74        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       52.01        34.29        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A222 TCGA-BG-A2AE TCGA-BG-A2L7 
       14.73        14.01        15.45         9.57        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       11.31        22.39        35.90        34.98        35.90        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       24.99        24.13        16.64        13.18        10.03         9.86 
TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
       46.95        24.33        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        97.41       114.90 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 
       85.84        82.39        81.57        72.72        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       89.59        63.58        83.64        86.99        66.48        16.83 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       29.95         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        3.68        29.33        32.58         0.66        15.72        36.10 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95        48.79         8.48        58.95 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JQ TCGA-DF-A2KN TCGA-DF-A2KU TCGA-DF-A2KV 
       15.88        18.84        17.29         2.20       100.83        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       35.38         9.37        23.38        79.10        58.95         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       45.57        16.04         7.36        16.80        10.92        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        50.73        35.15        38.07 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       46.42        26.96        22.26        38.47        51.09        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       33.34        19.27        22.03        16.11        32.78        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 
       37.05        19.33        22.82        20.05        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       32.52        11.38        14.14        14.70        16.96        68.38 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        25.22        96.69        59.01         9.34 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-KP-A3W0 
       28.93        30.67        59.28        41.56        17.75        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 
        9.47        18.21        23.24        21.30        38.70         8.19 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       17.16         6.97        22.65        39.95        24.95        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        20.75        18.28         0.23 

  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                          0.07                           0.13 
  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                         136.6                          225.5 
  DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE 
                         28.59                          29.95 
[1] "0.1 - 136.6 (28.6)" "0.1 - 225.5 (29.9)"
[1] "hr=" "2.1"
D99V2, binary
                                cls
clus                               0   1
  DEL PEAK 49(22Q12.1) MUTATED    50  35
  DEL PEAK 49(22Q12.1) WILD-TYPE 240 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 49(22Q12.1) MUTATED     50   35
  DEL PEAK 49(22Q12.1) WILD-TYPE  240  189
     clus
vv    DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE
  NO                            50                            240
  YES                           35                            189
[1] 2 2
[1] FALSE
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 49(22Q12.1) MUTATED                                        48
  DEL PEAK 49(22Q12.1) WILD-TYPE                                     356
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 49(22Q12.1) MUTATED                               9
  DEL PEAK 49(22Q12.1) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 49(22Q12.1) MUTATED                                  38
  DEL PEAK 49(22Q12.1) WILD-TYPE                                75
D99V3, multiclass
                                         clus
vv                                        DEL PEAK 49(22Q12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           48
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        DEL PEAK 49(22Q12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            356
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 49(22Q12.1) MUTATED    59   5   3  12
  DEL PEAK 49(22Q12.1) WILD-TYPE 312  17  13  28
D99V4, multiclass
    clus
vv   DEL PEAK 49(22Q12.1) MUTATED DEL PEAK 49(22Q12.1) WILD-TYPE
  R0                           59                            312
  R1                            5                             17
  R2                            3                             13
  RX                           12                             28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(100) Variable = DEL PEAK 50(22Q13.32) MUTATION ANALYSIS
D100V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 50(22Q13.32) MUTATED   101  38
  DEL PEAK 50(22Q13.32) WILD-TYPE 346  52
  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                            139                             398 
  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                             38                              52 
$`DEL PEAK 50(22Q13.32) MUTATED`
TCGA-2E-A9G8 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0LF 
       41.06        20.81        10.19       110.63        57.80        93.99 
TCGA-AX-A06B TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0KB 
       67.66        36.39        61.18        27.88         1.38        27.09 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-E6-A8L9 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A547 
       66.41        12.56        33.30        10.19        14.40        17.92 
TCGA-EY-A72D TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR 
        5.88        36.00        23.74        65.75        60.53        36.82 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP 
       37.91        17.59        36.33       118.19        25.51        14.96 
TCGA-A5-A7WK TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BD 
       18.41        20.25        14.43        21.14        19.79        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3TW 
       18.12        18.90         1.64        22.26        17.06        16.87 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ 
       21.99        63.91        45.53        48.79        97.71        46.78 
TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       36.13        35.74        37.78        34.65        25.51        32.02 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO 
        4.77        30.12        71.24        34.32         2.96        64.93 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82        20.52         0.30         0.26         0.30 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
       27.85        75.72        52.04       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0MT TCGA-BG-A0VZ 
       31.36       136.60        39.35        34.13        21.17        52.64 
TCGA-BG-A18C TCGA-BG-A2AD TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0U9 
       15.45        20.02        22.39        35.08        31.00        92.88 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15X TCGA-D1-A16I TCGA-D1-A16N 
       29.95         8.55        22.55        29.88        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW 
       18.67         3.95        14.73        28.08        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A3DG TCGA-D1-A3JQ TCGA-DF-A2KR TCGA-DF-A2KS TCGA-DF-A2L0 
       18.25         4.27        17.29        71.61       109.08        25.91 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A2P9 TCGA-EO-A1Y7 
       35.38         9.37        12.39        31.10        45.57        49.15 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ 
       51.42        27.16        22.26        16.34        54.15        23.90 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A2OQ 
       18.84        17.62        11.08        12.59        45.76        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       27.35        32.52        11.38        68.38        77.33        96.69 
TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
        9.34        59.28        78.38         1.74        17.75        14.04 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        38.70        22.59         8.19 
TCGA-SL-A6J9 
        0.07 

$`DEL PEAK 50(22Q13.32) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CR TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0MS 
       95.47        12.26        23.05        80.38        22.06        61.87 
TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO TCGA-D1-A102 TCGA-D1-A2G5 
       51.55        14.27         1.81        19.79         4.44        47.84 
TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ TCGA-EY-A215 TCGA-EY-A549 
       16.93         6.21        22.78        17.88        18.87        19.89 
TCGA-FI-A2CX TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5B-A90C TCGA-5S-A9Q8 
       66.77        13.84        73.32         0.43        39.52        10.29 
TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
      106.88       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GP TCGA-A5-A0GQ 
      112.54       105.37       123.68        74.10        46.55        73.87 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        54.02        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ 
       29.06        42.35        15.95        31.99        31.99        33.07 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A7WJ TCGA-AJ-A23O 
       66.15        28.64        24.72        34.95        11.21        10.26 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       35.15        34.36        33.90        14.66        22.49        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV 
       16.87        22.32        12.82        20.78         2.70        35.11 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
        0.13       129.80        23.31        86.07        48.03        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       90.97        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO 
       60.23        45.86        27.85        51.12        21.90         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        33.21        29.69        80.55        88.24        71.51 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H 
       35.34        45.99        79.46        49.87        57.47        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        61.08        43.82        40.11        77.39 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.28        32.91        26.37        25.91        34.09        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA 
       85.48        73.41        80.25        37.58        40.80        81.37 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        38.24        17.75        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.20         0.20         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        86.37        55.30        59.24        86.01        58.75 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       69.27        71.44        48.59        36.49        72.62        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      113.36        88.34        54.44        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MV TCGA-B5-A1MW 
       18.41        17.36        16.57       225.50        51.45        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       48.43        52.54        96.30        93.50        71.84        27.65 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        71.24        63.68        74.63        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       41.52        48.56        23.47        43.30        43.04        59.74 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 
       20.28        15.42        51.06        52.01        34.29        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A222 TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
        9.57        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       35.90        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        24.33        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
        4.80        77.95        61.87        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41       114.90        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI 
       73.25        59.51        89.59        63.58        83.64        86.99 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       66.48        16.83         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
        1.74        21.99        39.48        30.08         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY 
       11.15        24.30         2.33        22.92         1.41        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95        48.79 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KU 
        8.48        58.95        15.88        18.84         2.20       100.83 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30       110.10        23.38        79.10        58.95         2.37 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        10.92        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       34.39        50.73        35.15        38.07        46.42        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       38.47        51.09        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS 
       23.34        23.34        33.34        32.71        19.27        22.03 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A2OM 
       16.11        32.78        15.81        37.05        19.33        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D0 
       20.05        31.04        14.14        14.70        16.96        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
        7.99        25.22        59.01        28.93        30.67        41.56 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       13.28         9.47        21.30        17.16         6.97        22.65 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        24.95        23.64        14.83         4.44        20.75 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                           0.07                            0.13 
  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                          136.6                           225.5 
  DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE 
                          27.09                           30.74 
[1] "0.1 - 136.6 (27.1)" "0.1 - 225.5 (30.7)"
[1] "hr=" "2.4"
D100V2, binary
                                 cls
clus                                0   1
  DEL PEAK 50(22Q13.32) MUTATED    74  55
  DEL PEAK 50(22Q13.32) WILD-TYPE 216 169
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 50(22Q13.32) MUTATED     74   55
  DEL PEAK 50(22Q13.32) WILD-TYPE  216  169
     clus
vv    DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE
  NO                             74                             216
  YES                            55                             169
[1] 2 2
[1] FALSE
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 50(22Q13.32) MUTATED                                        57
  DEL PEAK 50(22Q13.32) WILD-TYPE                                     347
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 50(22Q13.32) MUTATED                              10
  DEL PEAK 50(22Q13.32) WILD-TYPE                            12
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 50(22Q13.32) MUTATED                                  73
  DEL PEAK 50(22Q13.32) WILD-TYPE                                40
D100V3, multiclass
                                         clus
vv                                        DEL PEAK 50(22Q13.32) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            57
  MIXED SEROUS AND ENDOMETRIOID                                      10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  73
                                         clus
vv                                        DEL PEAK 50(22Q13.32) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             347
  MIXED SEROUS AND ENDOMETRIOID                                        12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 50(22Q13.32) MUTATED    90   6   6  15
  DEL PEAK 50(22Q13.32) WILD-TYPE 281  16  10  25
D100V4, multiclass
    clus
vv   DEL PEAK 50(22Q13.32) MUTATED DEL PEAK 50(22Q13.32) WILD-TYPE
  R0                            90                             281
  R1                             6                              16
  R2                             6                              10
  RX                            15                              25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(101) Variable = DEL PEAK 51(XP21.1) MUTATION ANALYSIS
D101V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 51(XP21.1) MUTATED    58  29
  DEL PEAK 51(XP21.1) WILD-TYPE 389  61
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           87                           450 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           29                            61 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-2E-A9G8 TCGA-AP-A053 TCGA-AP-A05D TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2H8 
       41.06       110.63        57.80        67.66        23.05        61.18 
TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV 
       27.88         1.38        80.38        22.06        66.41        12.56 
TCGA-E6-A8L9 TCGA-EY-A547 TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-5B-A90C TCGA-A5-A0GN 
       33.30        17.92        36.00        23.74        39.52        60.53 
TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP 
       36.82        37.91        17.59        36.33       118.19        14.96 
TCGA-A5-A7WK TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3I9 TCGA-AJ-A3QS 
       18.41        14.43        34.16        18.12        17.06        16.87 
TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AW-A1PO 
       16.87        45.53        36.89        48.79        97.71         0.56 
TCGA-AX-A1C7 TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A3G4 TCGA-B5-A0K3 
       34.65        80.25         4.77        30.12         0.30        27.29 
TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       27.85       113.36        52.04        50.89        11.87        31.36 
TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-D1-A16I TCGA-D1-A16N 
       39.35        34.95        35.08        16.64        11.51        31.07 
TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3JQ 
        3.95        28.08        13.22         2.07         4.27        17.29 
TCGA-DF-A2KS TCGA-DF-A2L0 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y5 
      109.08        25.91         9.37        12.39       110.10        10.92 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GP 
       51.42        19.40        27.16        22.26        23.90        18.84 
TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A 
       11.08        20.05        29.10        27.35        11.38        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KP-A3W1 
       77.33        96.69        28.93        41.56        14.04         9.47 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
       18.21        23.24         4.44 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A1OK TCGA-A5-AB3J TCGA-AJ-A2QM TCGA-AJ-A3BG 
       88.18        60.53        30.15        16.83        29.39        18.08 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LF TCGA-AP-A0LS TCGA-AX-A06D TCGA-AX-A1CP 
       20.81        10.19        93.99        95.47        12.26        36.39 
TCGA-B5-A0KB TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A220 TCGA-BG-A221 TCGA-D1-A0ZO 
       27.09        61.87        51.55        14.27         1.81        19.79 
TCGA-D1-A102 TCGA-D1-A2G5 TCGA-D1-A3JP TCGA-EY-A1G7 TCGA-EY-A1GK TCGA-EY-A1GQ 
        4.44        47.84        16.93         6.21        22.78        17.88 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2CX 
       10.19        14.40        18.87        19.89         5.88        66.77 
TCGA-FI-A2D5 TCGA-FI-A2F4 TCGA-4E-A92E TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 
       13.84        73.32         0.43        10.29       106.88       149.56 
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE 
       37.02        83.51        17.85        32.78       112.54       105.37 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
      123.68        74.10        65.75        46.55        73.87        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       54.02        23.21        68.65        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A2K3 
       42.35        15.95        31.99        31.99        33.07        66.15 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A7WJ TCGA-AJ-A23M 
       28.64        24.72        34.95        25.51        11.21        20.25 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BI 
       10.26        21.14        19.79        35.15        34.36        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NC 
       33.90         1.64        14.66        22.49        22.26        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CV TCGA-AJ-A8CW 
       22.32        12.82        20.78         2.70        35.11         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
      129.80        21.99        23.31        86.07        48.03        63.91 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.62        20.91       125.42       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       66.25        36.36        46.72        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        80.78        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       90.97        55.89        31.30        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        60.23        45.86        27.85        51.12        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        13.58        33.21        29.69        80.55        88.24 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F 
       71.51        35.34        45.99        79.46        49.87        57.47 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        61.08        35.74        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        77.39        13.28        32.91        25.51 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       26.37        32.02        25.91        34.09        76.83        85.48 
TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       73.41        37.58        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        38.24        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        86.37        55.30        59.24        86.01 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       58.75        69.27        71.44        48.59        36.49        72.62 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       57.76        64.21        63.55        13.45        59.84       185.79 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
       88.34        75.72        54.44        73.64        61.68        85.78 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        77.23        73.28        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV 
       18.41        17.36        16.57       225.50       102.31        51.45 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        48.43        52.54       136.60        96.30        93.50 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       71.84        27.65        29.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        71.24        63.68 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       74.63        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        59.74        21.17        20.28        15.42        51.06 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       52.01        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A222 
       13.78        14.73        14.01        15.45        15.45         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       20.02        23.70        20.12        11.31        22.39        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98        35.90        31.00        31.76        24.99        24.13 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       13.18        10.03         9.86        46.95        24.33        85.55 
TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       78.21         4.80        77.95        61.87        67.99        96.49 
TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        92.88       114.90        85.84        82.39 
TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 
       81.57        72.72        73.25        59.51        89.59        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       83.64        86.99        66.48        16.83        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
        0.56         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
       21.99        39.48        30.08        29.88         1.91         3.68 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95        48.79         8.48        58.95        15.88 
TCGA-D1-A3DH TCGA-DF-A2KN TCGA-DF-A2KR TCGA-DF-A2KU TCGA-DF-A2KV TCGA-DF-A2KY 
       18.84         2.20        71.61       100.83        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        79.10        58.95         2.37        45.57 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        51.52        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       50.73        35.15        38.07        46.42        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       38.47        51.09        14.99        54.15        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       27.16        23.34        23.34        33.34        32.71        19.27 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        22.03        16.11        32.78        15.81        37.05 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       19.33        12.59        22.82        45.76        31.04        32.52 
TCGA-EY-A548 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D6 
       14.14        16.96        68.38        39.88         7.99        25.22 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       59.01         9.34        30.67        59.28        78.38         1.74 
TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       17.75        13.28        26.10        21.30        38.70        22.59 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        8.19        17.16         6.97        22.65        39.95        24.95 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        20.75        18.28         0.07         0.23 

  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                         0.30                          0.07 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                       118.19                        225.50 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                       27.290                        30.555 
[1] "0.3 - 118.2 (27.3)" "0.1 - 225.5 (30.6)"
[1] "hr=" "2.7"
D101V2, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    44  38
  DEL PEAK 51(XP21.1) WILD-TYPE 246 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     44   38
  DEL PEAK 51(XP21.1) WILD-TYPE  246  186
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  NO                           44                           246
  YES                          38                           186
[1] 2 2
[1] FALSE
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                        32
  DEL PEAK 51(XP21.1) WILD-TYPE                                     372
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 51(XP21.1) MUTATED                               4
  DEL PEAK 51(XP21.1) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                  52
  DEL PEAK 51(XP21.1) WILD-TYPE                                61
D101V3, multiclass
                                         clus
vv                                        DEL PEAK 51(XP21.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          32
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                52
                                         clus
vv                                        DEL PEAK 51(XP21.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           372
  MIXED SEROUS AND ENDOMETRIOID                                      18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP21.1) MUTATED    56   2   6   7
  DEL PEAK 51(XP21.1) WILD-TYPE 315  20  10  33
D101V4, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  R0                          56                           315
  R1                           2                            20
  R2                           6                            10
  RX                           7                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
