[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/11541775/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/11548534/transformed.cor.cli.txt"

nPatients in clinical file=514, in cluster file=539, common to both=505
[1] 100 505
[1] "AMP PEAK  1(1P35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           50                           455 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           50                           455 
[1] "AMP PEAK  2(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           65                           440 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           65                           440 
[1] "AMP PEAK  3(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           90                           415 
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           90                           415 
[1] "AMP PEAK  4(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                          225                           280 
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                          225                           280 
[1] "AMP PEAK  5(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                        239                         266 
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                        239                         266 
[1] "AMP PEAK  6(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                        202                         303 
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                        202                         303 
[1] "AMP PEAK  7(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                          112                           393 
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                          112                           393 
[1] "AMP PEAK  8(2Q13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                        109                         396 
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                        109                         396 
[1] "AMP PEAK  9(3P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           78                           427 
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           78                           427 
[1] "AMP PEAK 10(3P14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           60                           445 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           60                           445 
[1] "AMP PEAK 11(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          158                           347 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          158                           347 
[1] "AMP PEAK 12(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                          148                           357 
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                          148                           357 
[1] "AMP PEAK 13(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           51                           454 
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           51                           454 
[1] "AMP PEAK 14(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            83                            422 
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            83                            422 
[1] "AMP PEAK 15(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           50                           455 
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           50                           455 
[1] "AMP PEAK 16(6P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                          109                           396 
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                          109                           396 
[1] "AMP PEAK 17(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                           98                           407 
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                           98                           407 
[1] "AMP PEAK 18(6Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           80                           425 
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           80                           425 
[1] "AMP PEAK 19(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           82                           423 
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           82                           423 
[1] "AMP PEAK 20(8P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                           120                            385 
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                           120                            385 
[1] "AMP PEAK 21(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                           153                            352 
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                           153                            352 
[1] "AMP PEAK 22(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                           194                            311 
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                           194                            311 
[1] "AMP PEAK 23(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                           200                            305 
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                           200                            305 
[1] "AMP PEAK 24(9P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           61                           444 
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           61                           444 
[1] "AMP PEAK 25(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                           37                           468 
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                           37                           468 
[1] "AMP PEAK 26(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                           136                            369 
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                           136                            369 
[1] "AMP PEAK 27(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            48                            457 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            48                            457 
[1] "AMP PEAK 28(11Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            67                            438 
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            67                            438 
[1] "AMP PEAK 29(11Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            54                            451 
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            54                            451 
[1] "AMP PEAK 30(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            86                            419 
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            86                            419 
[1] "AMP PEAK 31(12Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             81                             424 
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             81                             424 
[1] "AMP PEAK 32(12Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            92                            413 
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            92                            413 
[1] "AMP PEAK 33(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                          56                          449 
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                          56                          449 
[1] "AMP PEAK 34(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            59                            446 
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            59                            446 
[1] "AMP PEAK 35(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             72                             433 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             72                             433 
[1] "AMP PEAK 36(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            36                            469 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            36                            469 
[1] "AMP PEAK 37(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            62                            443 
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            62                            443 
[1] "AMP PEAK 38(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            68                            437 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            68                            437 
[1] "AMP PEAK 39(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          69                          436 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          69                          436 
[1] "AMP PEAK 40(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                            94                            411 
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                            94                            411 
[1] "AMP PEAK 41(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             89                             416 
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             89                             416 
[1] "AMP PEAK 42(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            64                            441 
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            64                            441 
[1] "AMP PEAK 43(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            90                            415 
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            90                            415 
[1] "AMP PEAK 44(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                         106                          399 
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                         106                          399 
[1] "AMP PEAK 45(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                         110                          395 
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                         110                          395 
[1] "AMP PEAK 46(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                            140                             365 
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                            140                             365 
[1] "AMP PEAK 47(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                            140                             365 
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                            140                             365 
[1] "AMP PEAK 48(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                            138                             367 
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                            138                             367 
[1] "AMP PEAK 49(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            58                            447 
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            58                            447 
[1] "AMP PEAK 50(XP11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            82                            423 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            82                            423 
[1] "AMP PEAK 51(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         83                         422 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         83                         422 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            64                            441 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            64                            441 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            74                            431 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            74                            431 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           25                           480 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           25                           480 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           44                           461 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           44                           461 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           49                           456 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           49                           456 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           69                           436 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           69                           436 
[1] "DEL PEAK  7(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            40                            465 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            40                            465 
[1] "DEL PEAK  8(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           81                           424 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           81                           424 
[1] "DEL PEAK  9(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           83                           422 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           83                           422 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           94                           411 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           94                           411 
[1] "DEL PEAK 11(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          120                           385 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          120                           385 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          101                           404 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          101                           404 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         43                         462 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         43                         462 
[1] "DEL PEAK 14(7P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           67                           438 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           67                           438 
[1] "DEL PEAK 15(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            39                            466 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            39                            466 
[1] "DEL PEAK 16(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           52                           453 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           52                           453 
[1] "DEL PEAK 17(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           61                           444 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           61                           444 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          106                           399 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          106                           399 
[1] "DEL PEAK 19(8P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          104                           401 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          104                           401 
[1] "DEL PEAK 20(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         70                         435 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         70                         435 
[1] "DEL PEAK 21(9Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          117                           388 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          117                           388 
[1] "DEL PEAK 22(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          119                           386 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          119                           386 
[1] "DEL PEAK 23(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             68                             437 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             68                             437 
[1] "DEL PEAK 24(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            94                            411 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            94                            411 
[1] "DEL PEAK 25(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            64                            441 
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            64                            441 
[1] "DEL PEAK 26(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          86                          419 
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          86                          419 
[1] "DEL PEAK 27(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            46                            459 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            46                            459 
[1] "DEL PEAK 28(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             56                             449 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             56                             449 
[1] "DEL PEAK 29(13Q11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          86                          419 
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          86                          419 
[1] "DEL PEAK 30(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            93                            412 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            93                            412 
[1] "DEL PEAK 31(14Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            67                            438 
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            67                            438 
[1] "DEL PEAK 32(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           128                            377 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           128                            377 
[1] "DEL PEAK 33(15Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                         107                          398 
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                         107                          398 
[1] "DEL PEAK 34(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            83                            422 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            83                            422 
[1] "DEL PEAK 35(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                         141                          364 
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                         141                          364 
[1] "DEL PEAK 36(16Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                           144                            361 
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                           144                            361 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           152                            353 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           152                            353 
[1] "DEL PEAK 38(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                           110                            395 
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                           110                            395 
[1] "DEL PEAK 39(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                           115                            390 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                           115                            390 
[1] "DEL PEAK 40(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            95                            410 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            95                            410 
[1] "DEL PEAK 41(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                            100                             405 
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                            100                             405 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            82                            423 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            82                            423 
[1] "DEL PEAK 43(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          87                          418 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          87                          418 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           141                            364 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           141                            364 
[1] "DEL PEAK 45(19P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          52                          453 
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          52                          453 
[1] "DEL PEAK 46(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             58                             447 
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             58                             447 
[1] "DEL PEAK 47(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            31                            474 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            31                            474 
[1] "DEL PEAK 48(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            129                             376 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            129                             376 
[1] "DEL PEAK 49(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           77                           428 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           77                           428 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 505 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
          33           NA         4549         1126         2540           NA 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
         997           98         3205         2656         2254         1750 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
        2000         1841         1841         1416         1167         1120 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
         860          633          706         2088          607          535 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
         596          749          884         1288          485          241 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
         348         1105          292          244         2769         1409 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
          NA          162          157          223          455           36 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
          33           60           12          602           26           73 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BH TCGA-AJ-A3BI 
          92           15           34           23           NA           68 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
          51           NA          446          684          677           39 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
          28         1125          628           41          475           23 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
          59          485           57          513           52           71 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
          30           82            4         2545           NA          181 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
          NA         2618          250         1199         1758         1385 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
        1122          239          371          636           NA         3815 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
        3589         3357          103         1921           NA         2972 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
         965         2554          825         2510           NA         1875 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
        2457         1918         1497          763         2180         1836 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
        1700          952           NA         1276         1495          204 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
         940          317          847          494          555         1026 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
          17           NA          603          903         2079         2191 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
        1413         1075         1399         2025         1064         1640 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
          NA         1554          833          913         1845         1065 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
         868         1149         1333         1220         2004          404 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
         584          516          412          464          617          378 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
         610         2337         2207         1646         2053          764 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
        1107          337           NA           NA         2167         1020 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
        1861         2090         1016         1232          589          801 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
         540          831           NA           NA         1177            7 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
           3           10            4            6           NA            1 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
           4           NA            7           36          254          440 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
           4         2445         1731         1422         1312         1483 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
        1237         1360          990          871          862          928 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
         788          700          544          418          520          543 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
         335          125          265         5651         3448         2687 
TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
        2303         1656         1396         1337         1232         1120 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
         976         1019          832          509          595          593 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
         560          528          504         5835           NA           NA 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
         438          447          356           NA          465          389 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 
        3536         2929         2397         1890         1007          153 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        1249         1038         1063          566          614          588 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
         637         1071         1064          241         1167         1110 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
         860           NA         1263         1477           NA           NA 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
        1309         1196          937          644          617          469 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
         742          811          497         1043         1601         1607 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
        1721          451          382          419          448          426 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
         470          470          434           55          291         1085 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
         721          612          344          207         1092         1064 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
         189          311          309          966          760          734 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
         506          401          305          300           NA          714 
TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
        2602         2379           NA         2371         1882         2068 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
        2935           NA         2963         2044         2687         2611 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
        2506         2481         2212         2228         1810         1910 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
        1934         1507         1921         2022          512          602 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
         911          260           17          148          872          728 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
         686           53          135          669         1201          915 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
         909           NA          112          892          991           20 
TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
         478         1098         1135         1106         1141         1119 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
          NA           NA          910          945         1023          324 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
          21          568           43          111          532          594 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
         202          917          548          206           48          213 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
          30          926           39          852          854          802 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
         311           46           54           NA          739           71 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
         697           43          402           22          555          513 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
         548           63          458           32           NA          107 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        1260           NA         1365            8          130          125 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
         826          496         1195         1114          739         1076 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
          NA           NA           NA         2797          711         1471 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
         519           NA          203          740          487          224 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
         511          332          572         1147          972         1066 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
        1004          825         1752          754          985           NA 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
        1046          589         1069          392          826          820 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
         677          497           NA           NA          138          248 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
         741          826          710          710          727          693 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
         425          210          586          573          544          536 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
         459          490          378          481          260          197 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
         588          383          110          438          574          694 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
         409         1392          944          885          832          421 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
         196          545           65          212          113          161 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
         179         1217         1064         1034         1095           NA 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
          NA          273         2941         1795          276           NA 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
         881          761          791           NA         1369           53 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
         400           74          329          277          729          393 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
         213          342          212          573         1215          128 
TCGA-QS-A5YR 
         168 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=411,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "HISTOLOGICAL.TYPE"                     
[3] "RADIATIONS.RADIATION.REGIMENINDICATION"
[4] "COMPLETENESS.OF.RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 505 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=5, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P35.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P35.2) MUTATED    39  10
  AMP PEAK  1(1P35.2) WILD-TYPE 404  50
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           49                           454 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           10                            50 
$`AMP PEAK  1(1P35.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-AJ-A3BF 
       37.02        65.75        19.96        11.44        91.04         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 
        2.24         1.64        39.42        57.80        45.53        48.79 
TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1CF TCGA-AX-A2H5 
       97.71        18.25        33.73        37.78        76.83        71.24 
TCGA-AX-A2HF TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A0JN TCGA-B5-A0K3 
       19.36        20.52         0.13         0.23        80.38        23.01 
TCGA-B5-A0K8 TCGA-B5-A1MS TCGA-B5-A3S1 TCGA-BG-A18C TCGA-BK-A4ZD TCGA-BS-A0U9 
       17.85       102.31         5.03        15.45        16.64        67.20 
TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NX 
       22.55        11.51        31.07         6.77        28.08        18.25 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GW 
       18.81        37.71        22.26        16.34        23.90         8.55 
TCGA-EY-A3L3 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 
       27.35        34.98        36.00        96.69        59.01        26.01 
TCGA-PG-A5BC 
       10.82 

$`AMP PEAK  1(1P35.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18         1.08         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        2.40         3.02         0.49         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
        1.35        15.62         0.76         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87         1.71         2.33         0.99         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       36.89         7.86        12.20        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        30.12        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       68.71        33.40        40.50        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.20         0.03         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        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        23.47        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        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
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         1.41         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        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-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       27.16        26.96         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
        6.90        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        3.62        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
        6.97         3.72         5.29         5.88        40.01        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        41.06        45.01         1.74        13.15         2.43 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
        9.11        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                       102.31                        191.84 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                       23.900                        22.635 
[1] "0.1 - 102.3 (23.9)" "0.0 - 191.8 (22.6)"
[1] "hr=" "1.7"
D1V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  1(1P35.2) MUTATED                                        14
  AMP PEAK  1(1P35.2) WILD-TYPE                                     366
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  1(1P35.2) MUTATED                               5
  AMP PEAK  1(1P35.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  1(1P35.2) MUTATED                                  31
  AMP PEAK  1(1P35.2) WILD-TYPE                                73
D1V3, multiclass
                                         clus
vv                                        AMP PEAK  1(1P35.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          14
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                31
                                         clus
vv                                        AMP PEAK  1(1P35.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           366
  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"
D1V4, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P35.2) MUTATED    15  35
  AMP PEAK  1(1P35.2) WILD-TYPE 123 332
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P35.2) MUTATED     15   35
  AMP PEAK  1(1P35.2) WILD-TYPE  123  332
     clus
vv    AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE
  NO                           15                           123
  YES                          35                           332
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P35.2) MUTATED    32   2   2   5
  AMP PEAK  1(1P35.2) WILD-TYPE 319  20  15  25
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE
  R0                          32                           319
  R1                           2                            20
  R2                           2                            15
  RX                           5                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P35.2) MUTATED                                  0     1
  AMP PEAK  1(1P35.2) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P35.2) MUTATED                          13
  AMP PEAK  1(1P35.2) WILD-TYPE                        77
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P35.2) MUTATED                                           2    28
  AMP PEAK  1(1P35.2) WILD-TYPE                                         7   329
D1V6, multiclass
                                           clus
vv                                          AMP PEAK  1(1P35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              28
                                           clus
vv                                          AMP PEAK  1(1P35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            77
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               329
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P35.2) MUTATED     2  31
  AMP PEAK  1(1P35.2) WILD-TYPE  11 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P35.2) MUTATED      2   31
  AMP PEAK  1(1P35.2) WILD-TYPE   11  319
                        clus
vv                       AMP PEAK  1(1P35.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          31
                        clus
vv                       AMP PEAK  1(1P35.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           319
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1P34.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1P34.2) MUTATED    51  13
  AMP PEAK  2(1P34.2) WILD-TYPE 392  47
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           64                           439 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           13                            47 
$`AMP PEAK  2(1P34.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       37.02        65.75        11.44        14.96         1.18         1.08 
TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05H 
        0.49         0.76         1.71         0.99        21.99        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IU 
       48.79       125.42        18.25        33.73        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       37.78        16.96        76.83        36.39        11.08        30.12 
TCGA-AX-A2H5 TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0JN TCGA-B5-A0KB 
       71.24        20.52         0.03         0.13        80.38         4.11 
TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A4ZD TCGA-BS-A0U9 
       75.72         5.03        34.13        15.45        16.64        67.20 
TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A2G7 TCGA-DI-A1NO 
       22.55        11.51        31.07         6.77        44.88         9.37 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ 
       18.81        37.71        34.39        22.26        16.34        23.90 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON 
       15.81         8.55        12.59         3.62        14.40        13.45 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       29.10         6.44        34.98        36.00        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ 
        9.07        25.02        26.01        13.15 

$`AMP PEAK  2(1P34.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        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         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        7.33         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       16.87         2.33         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
        7.86        12.20        20.91       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       67.50        25.12         4.77        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.20         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        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        23.47        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        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
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         1.41         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-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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
       41.42         8.48         0.26         4.27         4.11        27.16 
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-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       32.38        19.40        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       26.96         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       12.43         6.48        19.33        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        27.35        13.84        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 
        3.72         5.29         5.88        40.01        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-FI-A3PX 
       13.84         8.98        28.93        28.96        41.06        45.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        1.74         2.43        10.82         9.11        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       21.255                        23.210 
[1] "0.0 - 125.4 (21.3)" "0.1 - 191.8 (23.2)"
[1] "hr=" "2"  
D2V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  2(1P34.2) MUTATED                                        19
  AMP PEAK  2(1P34.2) WILD-TYPE                                     361
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  2(1P34.2) MUTATED                               7
  AMP PEAK  2(1P34.2) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  2(1P34.2) MUTATED                                  39
  AMP PEAK  2(1P34.2) WILD-TYPE                                65
D2V3, multiclass
                                         clus
vv                                        AMP PEAK  2(1P34.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          19
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                39
                                         clus
vv                                        AMP PEAK  2(1P34.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           361
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    14  51
  AMP PEAK  2(1P34.2) WILD-TYPE 124 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     14   51
  AMP PEAK  2(1P34.2) WILD-TYPE  124  316
     clus
vv    AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  NO                           14                           124
  YES                          51                           316
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P34.2) MUTATED    38   4   5   6
  AMP PEAK  2(1P34.2) WILD-TYPE 313  18  12  24
D2V5, multiclass
    clus
vv   AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  R0                          38                           313
  R1                           4                            18
  R2                           5                            12
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1P34.2) MUTATED                                  0     1
  AMP PEAK  2(1P34.2) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1P34.2) MUTATED                          19
  AMP PEAK  2(1P34.2) WILD-TYPE                        71
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1P34.2) MUTATED                                           2    37
  AMP PEAK  2(1P34.2) WILD-TYPE                                         7   320
D2V6, multiclass
                                           clus
vv                                          AMP PEAK  2(1P34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              37
                                           clus
vv                                          AMP PEAK  2(1P34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED     2  42
  AMP PEAK  2(1P34.2) WILD-TYPE  11 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED      2   42
  AMP PEAK  2(1P34.2) WILD-TYPE   11  308
                        clus
vv                       AMP PEAK  2(1P34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK  2(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           308
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1P22.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(1P22.3) MUTATED    77  13
  AMP PEAK  3(1P22.3) WILD-TYPE 366  47
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           90                           413 
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           13                            47 
$`AMP PEAK  3(1P22.3) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A3LP TCGA-AJ-A23M 
       37.02        83.51        60.53        11.44        14.96         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A6NU 
        1.97         0.85         0.49         1.64         0.76         0.99 
TCGA-AP-A051 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LF 
       83.67        45.53        48.79       125.42       110.37         3.39 
TCGA-AP-A0LL TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 
       83.97        31.30        35.54        10.42        16.24        18.25 
TCGA-AP-A5FX TCGA-AX-A060 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 
       33.73        35.34        34.98        35.01        37.78        65.88 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A3FS TCGA-AX-A3G1 
       11.08         4.77        61.18        68.71         0.23        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0K7 TCGA-B5-A0K8 
        0.03         0.13        80.38        56.91        17.10        17.85 
TCGA-B5-A11I TCGA-B5-A11Q TCGA-B5-A11Z TCGA-B5-A1MS TCGA-B5-A1MZ TCGA-B5-A3S1 
       75.72        32.09        17.36       102.31        15.29         5.03 
TCGA-B5-A5OD TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A3EW 
       34.13        21.17        15.42        52.83        15.45        11.31 
TCGA-BK-A13B TCGA-BK-A4ZD TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-D1-A160 
       31.76        16.64        30.74        67.20        72.72         3.68 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17A TCGA-D1-A2G5 TCGA-D1-A3DA TCGA-DI-A0WH 
       11.51        18.67         1.58        41.42         0.26        16.31 
TCGA-DI-A1NO TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GD 
        9.37        34.39        22.26        16.34         4.54         8.15 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A212 
       23.90        19.27        17.88        16.11        12.43         3.62 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU 
       13.45        45.76        29.10         3.72        36.00        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       59.01        28.96        25.02        23.97        12.92         7.00 

$`AMP PEAK  3(1P22.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88       149.56        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        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-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.08         0.39        19.79         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76         2.24         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
       20.91       117.99        63.16        36.36        97.71        31.73 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DQ 
       49.22        25.08        71.67        60.36        55.89        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A05S 
       49.15         6.71        30.90        27.85         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 
       19.82        29.69        68.35        72.03        46.45        45.99 
TCGA-AX-A063 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 
       60.66        28.54        43.82        40.11        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       30.12        71.24        33.53        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.10         0.33         0.13         0.20         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47         0.13        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K9 TCGA-B5-A0KB 
       25.91        23.01        17.88        13.74        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        36.82        33.50        27.35        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.56        19.50        18.41        16.57       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.40        14.70        11.70        11.87        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        78.81        62.14        33.11        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.16        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        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF 
       61.87        67.99        96.49        97.41        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 
        1.91        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         1.41         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         6.77 
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-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
        3.52         8.48        44.88         4.27         4.11        27.16 
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 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       24.33        16.01         7.36        16.80        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        32.38        19.40        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GF 
       27.16        26.96         6.21        14.99        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        22.78        13.97         6.90        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        15.09        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        14.40        18.87        22.82        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       13.84         6.44        17.92         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        34.98        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        8.98         9.07        28.93        26.01        41.06        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 
        1.74        13.15         2.43        10.82         9.11        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                        18.97                         23.31 
[1] "0.0 - 125.4 (19.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.3"
D3V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  3(1P22.3) MUTATED                                        53
  AMP PEAK  3(1P22.3) WILD-TYPE                                     327
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  3(1P22.3) MUTATED                               5
  AMP PEAK  3(1P22.3) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  3(1P22.3) MUTATED                                  32
  AMP PEAK  3(1P22.3) WILD-TYPE                                72
D3V3, multiclass
                                         clus
vv                                        AMP PEAK  3(1P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          53
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                32
                                         clus
vv                                        AMP PEAK  3(1P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           327
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D3V4, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P22.3) MUTATED    22  68
  AMP PEAK  3(1P22.3) WILD-TYPE 116 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P22.3) MUTATED     22   68
  AMP PEAK  3(1P22.3) WILD-TYPE  116  299
     clus
vv    AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE
  NO                           22                           116
  YES                          68                           299
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1P22.3) MUTATED    60   3   2   6
  AMP PEAK  3(1P22.3) WILD-TYPE 291  19  15  24
D3V5, multiclass
    clus
vv   AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE
  R0                          60                           291
  R1                           3                            19
  R2                           2                            15
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(1P22.3) MUTATED                                  1     2
  AMP PEAK  3(1P22.3) WILD-TYPE                                3    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1P22.3) MUTATED                          21
  AMP PEAK  3(1P22.3) WILD-TYPE                        69
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1P22.3) MUTATED                                           2    60
  AMP PEAK  3(1P22.3) WILD-TYPE                                         7   297
D3V6, multiclass
                                           clus
vv                                          AMP PEAK  3(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              60
                                           clus
vv                                          AMP PEAK  3(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            69
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               297
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P22.3) MUTATED     0  60
  AMP PEAK  3(1P22.3) WILD-TYPE  13 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P22.3) MUTATED      0   60
  AMP PEAK  3(1P22.3) WILD-TYPE   13  290
                        clus
vv                       AMP PEAK  3(1P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          60
                        clus
vv                       AMP PEAK  3(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           290
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(1Q21.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(1Q21.3) MUTATED   190  34
  AMP PEAK  4(1Q21.3) WILD-TYPE 253  26
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                          224                           279 
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                           34                            26 
$`AMP PEAK  4(1Q21.3) MUTATED`
TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       87.32        57.53        60.53        36.82        28.27        20.81 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M 
       11.44         9.60         8.02        46.32        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
        1.08         1.97         0.85         0.49         1.12         2.24 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.64        22.26         0.92        36.99         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW 
        0.76         1.87        16.87         1.71         0.99         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H 
       83.67        21.99         5.95        23.31        39.42        45.53 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LO TCGA-AP-A1DM 
        3.39        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        10.42        16.24        18.25        33.73 
TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
       13.58        68.35        72.03        46.45        35.34        66.58 
TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C8 TCGA-AX-A1CA 
       34.98        35.01        37.78        65.88        13.55        20.28 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 
       76.83        72.56        54.12        67.50        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2IN 
       71.24        33.53        61.18        68.71        17.75        31.13 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI 
       20.52         0.03         0.13         1.18        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K4 
       80.38        56.91        43.13        40.67        28.34        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A11Q 
       13.74        17.10        11.01        75.72        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1MZ 
       33.50        27.35        17.36       102.31        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LX TCGA-BG-A0M0 
       12.79         5.03        41.06        34.13        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MO TCGA-BG-A0MQ 
       20.94        35.21        34.98         7.92        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A3EW 
       52.83        13.78        15.45         1.81         9.57        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       35.90        10.22        10.16        31.76        24.99        16.64 
TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0VI TCGA-D1-A0ZN 
       61.87        30.74        67.20        72.72        63.16        16.83 
TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I 
        8.55         0.56         4.44         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         1.41        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-A2G5 
       26.37        10.22        11.15        18.02         2.07        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48        44.88         0.26         4.11        27.16        16.31 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A2P9 TCGA-E6-A8L9 
        9.37        12.39        91.96        48.36         6.67        24.33 
TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AZ 
        7.36        10.92        37.71        24.79        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        22.26        16.34         6.21         4.54         8.15 
TCGA-EY-A1GF TCGA-EY-A1GK TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       27.16        22.78        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A210 
       15.09        16.11        12.43        15.81         6.48        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
        3.62        14.40        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 
       27.35         6.44         6.97         3.72         5.29        36.00 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A7D5 TCGA-PG-A914 
       45.01         1.74        13.15         2.43        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A917 
        7.00         6.97 

$`AMP PEAK  4(1Q21.3) WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM 
      106.88         3.22       105.37        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       46.55        38.37        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       36.33        91.04        28.64         5.33         5.16         7.33 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK 
        0.39        19.79         2.40         3.02         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       14.66        22.49         1.28        20.65         1.94        15.95 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        2.33         2.70        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
        7.86        63.16        31.73        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AW-A1PO 
       41.95        49.15         6.71        30.90        27.85         0.56 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       19.82        29.69        45.99        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        28.54        43.82        40.11 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        16.96        15.25        12.43        20.05 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       25.12        36.39        30.12        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        27.32         2.96        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JS 
        0.33         0.13         0.20         0.23         8.35        46.75 
TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 
       48.76        44.71        32.55        28.64        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       23.01        17.85         4.11         8.71       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        45.90        43.96        40.50        16.73 
TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MU 
       19.56        19.50        18.41        16.57       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.40        14.70        11.70       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M8 
       62.14        33.11        34.95        18.61        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        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-A0YV 
       16.34        34.29        52.64        56.58        14.83        12.56 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.73        14.01        15.45        14.27        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A26L TCGA-BK-A56F 
       20.12         6.81        34.98         6.21        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        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA 
        4.80        77.95        67.99        96.49        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZS 
       63.58        49.55        66.48        19.79        29.95         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-A161 TCGA-D1-A163 TCGA-D1-A167 
       30.08        29.88         1.91        29.33        32.58        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-A16X 
       29.92        31.07        33.63        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A179 TCGA-D1-A17C TCGA-D1-A17D 
       17.49        19.53         6.64         6.77         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
        1.28        28.01        28.08         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG 
       16.87        15.06         1.05         3.95         3.52         4.27 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        35.38        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
       17.06         2.37        16.01        16.80        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        32.38        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH 
       19.36        35.15        12.89        14.99        24.36        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GW TCGA-EY-A1H0 
       23.34        23.90        13.97         6.90         8.55        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A72D 
       18.87        22.82        13.84        17.92         2.14         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-QF-A5YS 
       96.69        26.01        10.82         9.11        11.24        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                       149.56                        191.84 
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                        19.76                         24.13 
[1] "0.0 - 149.6 (19.8)" "0.1 - 191.8 (24.1)"
[1] "hr=" "1.8"
D4V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  4(1Q21.3) MUTATED                                       148
  AMP PEAK  4(1Q21.3) WILD-TYPE                                     232
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  4(1Q21.3) MUTATED                              10
  AMP PEAK  4(1Q21.3) WILD-TYPE                            11
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  4(1Q21.3) MUTATED                                  67
  AMP PEAK  4(1Q21.3) WILD-TYPE                                37
D4V3, multiclass
                                         clus
vv                                        AMP PEAK  4(1Q21.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         148
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                67
                                         clus
vv                                        AMP PEAK  4(1Q21.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           232
  MIXED SEROUS AND ENDOMETRIOID                                      11
  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"
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q21.3) MUTATED    57 168
  AMP PEAK  4(1Q21.3) WILD-TYPE  81 199
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q21.3) MUTATED     57  168
  AMP PEAK  4(1Q21.3) WILD-TYPE   81  199
     clus
vv    AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE
  NO                           57                            81
  YES                         168                           199
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(1Q21.3) MUTATED   159   9  10  13
  AMP PEAK  4(1Q21.3) WILD-TYPE 192  13   7  17
D4V5, multiclass
    clus
vv   AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE
  R0                         159                           192
  R1                           9                            13
  R2                          10                             7
  RX                          13                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(1Q21.3) MUTATED                                  2     5
  AMP PEAK  4(1Q21.3) WILD-TYPE                                2    14
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(1Q21.3) MUTATED                          53
  AMP PEAK  4(1Q21.3) WILD-TYPE                        37
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(1Q21.3) MUTATED                                           2   152
  AMP PEAK  4(1Q21.3) WILD-TYPE                                         7   205
D4V6, multiclass
                                           clus
vv                                          AMP PEAK  4(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          53
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                             152
                                           clus
vv                                          AMP PEAK  4(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                14
  BLACK OR AFRICAN AMERICAN                                            37
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               205
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q21.3) MUTATED     4 160
  AMP PEAK  4(1Q21.3) WILD-TYPE   9 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q21.3) MUTATED      4  160
  AMP PEAK  4(1Q21.3) WILD-TYPE    9  190
                        clus
vv                       AMP PEAK  4(1Q21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         160
                        clus
vv                       AMP PEAK  4(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           190
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(1Q22) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(1Q22) MUTATED   200  38
  AMP PEAK  5(1Q22) WILD-TYPE 243  22
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                        238                         265 
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                         38                          22 
$`AMP PEAK  5(1Q22) MUTATED`
TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       149.56        37.02        83.51        17.85        32.78 
TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       87.32        57.53        60.53        36.82        28.27        20.81 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 
       11.44        36.33         9.60         8.02        46.32        28.64 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A3BD 
       14.96         1.18         1.08         1.97         0.85         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.12         2.24         1.64        22.26         0.92        36.99 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        1.35        15.62         0.76         1.87        16.87         1.71 
TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        0.99         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       39.42        45.53        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LO 
      110.37         3.39        36.36        97.71        83.97        33.40 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 
       55.89        31.30        35.54        10.42        16.24        18.25 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       33.73        13.58        68.35        72.03        46.45        35.34 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       66.58        34.98        35.01        28.54        37.78        65.88 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CI 
       16.96        13.55        15.25        20.28        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        11.08        30.12        71.24        33.53 
TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FX 
       68.71        19.36        17.75        31.13        38.70         0.13 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI 
       20.52         0.03         0.13         1.18        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K3 
       80.38        56.91        43.13        40.67        28.34        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11P 
       17.88        13.74        17.10        11.01         4.11        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MS TCGA-B5-A1MU 
       32.09        33.50        27.35        17.36       102.31        50.89 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       11.87        15.29        12.79         5.03        41.06        34.13 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C 
       24.39        26.66        52.83        12.56        13.78        15.45 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 
        1.81         9.57        11.31        35.90        10.22        10.16 
TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U7 
       31.76        24.99        24.13        16.64        61.87        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZQ 
       97.41        67.20        72.72        63.16        16.83         8.55 
TCGA-D1-A0ZR TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16O 
        0.56         4.44         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         1.41        30.15        18.02         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
       18.02         2.07        41.42         8.48         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
        4.11        27.16        16.31         9.37        12.39        91.96 
TCGA-E6-A1LZ TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       48.36         6.67        24.33         7.36        10.92        37.71 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       24.79        34.39        27.16        26.96        22.26         6.21 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF TCGA-EY-A1GK TCGA-EY-A1GO TCGA-EY-A1GP 
        4.54         8.15        27.16        22.78        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO 
        6.48        12.59         3.62        14.40        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A549 TCGA-EY-A54A 
       31.04        29.10        27.35         6.44         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        5.29        36.00        59.01         9.07        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       25.02        26.01        41.06        45.01         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 
        2.43        23.97        12.92         6.97 

$`AMP PEAK  5(1Q22) WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ TCGA-A5-A0GM 
      106.88         3.22       105.37        74.10        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       46.55        38.37        23.21        68.65        19.96        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         7.92 
TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A2QK TCGA-AJ-A2QL 
       91.04         5.33         5.16         7.33         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40         3.02         0.76         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DW TCGA-AJ-A8CT 
        1.28        20.65         1.94        15.95         2.33         2.70 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0L9 
       86.07         8.22        57.80        36.89         7.86       125.42 
TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       63.16        31.73        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DQ 
       63.06        49.22        25.08        71.67        60.36        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A05T 
       49.15         6.71        30.90        27.85         0.56        19.82 
TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       29.69        45.99        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 
       30.02        60.66        43.82        40.11        13.28        19.20 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H8 
       12.43        20.05        25.12        36.39         4.77        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A3FS 
       33.40        40.50        26.33        27.32         2.96         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JS 
        0.10         0.33         0.20         0.23         8.35        46.75 
TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 
       48.76        44.71        32.55        28.64        30.51        25.91 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85         8.71       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        45.90        43.96        40.50        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       191.84        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       11.70       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.95        18.61        38.37        36.49        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0VW TCGA-BG-A0VX 
       41.52        48.56        23.47        43.30        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       52.64        56.58        14.83        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA 
       14.27        35.67        23.70        20.12         6.81        34.98 
TCGA-BK-A0CB TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA 
        6.21        13.18        10.03         9.86        46.95        23.47 
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-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP 
       62.79        63.58        49.55        66.48        19.79        29.95 
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-A161 TCGA-D1-A163 
       39.48        30.08        29.88         1.91        29.33        32.58 
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-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       27.42        29.92        31.07        10.65         0.69         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       17.49        19.53         6.64         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
       28.01         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        13.22         0.72        16.87        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        3.95         3.52        44.88        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ 
       35.38        31.10        23.38        17.06         2.37        16.01 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        18.81        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        32.38        19.40        19.36        35.15        12.89 
TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       16.34        14.99        24.36        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM 
       13.97         6.90         8.55        19.33        18.87        22.82 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       13.84        17.92         2.14         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-PG-A5BC 
       33.99         7.99        13.84         8.98        96.69        10.82 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        9.11         7.00        11.24        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                     149.56                      191.84 
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                     20.235                      24.300 
[1] "0.0 - 149.6 (20.2)" "0.1 - 191.8 (24.3)"
[1] "hr=" "2.2"
D5V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  5(1Q22) MUTATED                                       155
  AMP PEAK  5(1Q22) WILD-TYPE                                     225
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  5(1Q22) MUTATED                              10
  AMP PEAK  5(1Q22) WILD-TYPE                            11
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  5(1Q22) MUTATED                                  74
  AMP PEAK  5(1Q22) WILD-TYPE                                30
D5V3, multiclass
                                         clus
vv                                        AMP PEAK  5(1Q22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                       155
  MIXED SEROUS AND ENDOMETRIOID                                  10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              74
                                         clus
vv                                        AMP PEAK  5(1Q22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         225
  MIXED SEROUS AND ENDOMETRIOID                                    11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q22) MUTATED    61 178
  AMP PEAK  5(1Q22) WILD-TYPE  77 189
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q22) MUTATED     61  178
  AMP PEAK  5(1Q22) WILD-TYPE   77  189
     clus
vv    AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE
  NO                         61                          77
  YES                       178                         189
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(1Q22) MUTATED   164  11  12  14
  AMP PEAK  5(1Q22) WILD-TYPE 187  11   5  16
D5V5, multiclass
    clus
vv   AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE
  R0                       164                         187
  R1                        11                          11
  R2                        12                           5
  RX                        14                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(1Q22) MUTATED                                  2     5
  AMP PEAK  5(1Q22) WILD-TYPE                                2    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(1Q22) MUTATED                          53
  AMP PEAK  5(1Q22) WILD-TYPE                        37
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(1Q22) MUTATED                                           2   167
  AMP PEAK  5(1Q22) WILD-TYPE                                         7   190
D5V6, multiclass
                                           clus
vv                                          AMP PEAK  5(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                        53
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                           167
                                           clus
vv                                          AMP PEAK  5(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          37
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             190
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q22) MUTATED     5 170
  AMP PEAK  5(1Q22) WILD-TYPE   8 180
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q22) MUTATED      5  170
  AMP PEAK  5(1Q22) WILD-TYPE    8  180
                        clus
vv                       AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             5                           8
  NOT HISPANIC OR LATINO                       170                         180
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(1Q44) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(1Q44) MUTATED   172  29
  AMP PEAK  6(1Q44) WILD-TYPE 271  31
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                        201                         302 
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                         29                          31 
$`AMP PEAK  6(1Q44) MUTATED`
TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GG 
        1.08       149.56        83.51        17.85        32.78        87.32 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        65.75        60.53        36.82        28.27        20.81 
TCGA-A5-A0GX TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
       68.65        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       28.64        14.96         1.97         2.24         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS 
        0.92        36.99         1.35         0.76         1.87        16.87 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05D TCGA-AP-A05P 
        0.13        83.67        21.99        23.31        57.80        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37         3.39        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-A1DQ TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       41.95        10.42        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 
       13.58        72.03        46.45        35.34        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C8 
       53.92        35.01        28.54        37.78        65.88        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        20.28        76.83        72.56        54.12        67.50 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A2HK 
       11.08         4.77        33.53        68.71        17.75         2.96 
TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 
       38.70         0.13        20.52         0.03         0.13         1.18 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV TCGA-B5-A0K0 
       14.47         0.13        56.91        43.13        40.67        28.34 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z 
       75.72        36.82        32.09        33.50        27.35        17.36 
TCGA-B5-A1MU TCGA-B5-A1MZ TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LX TCGA-BG-A0M0 
       50.89        15.29         5.03        41.06        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MO 
       20.94        35.21        34.98         7.92        36.49        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A3EW 
       26.66        52.83        13.78         1.81         9.57        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        10.22        10.16        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        67.20        72.72        59.51        63.16 
TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A165 
       16.83         8.55         0.56         4.44         3.68         0.66 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       11.51        18.67        30.15        18.02         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       41.42         8.48         0.26         4.11        27.16        16.31 
TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AZ TCGA-EY-A1G7 
        6.67         7.36        10.92        24.79        27.16         6.21 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF TCGA-EY-A1GK TCGA-EY-A1GO TCGA-EY-A1GP 
        4.54         8.15        27.16        22.78        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       17.88        17.62        15.09        16.11        12.43         6.48 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR 
        3.62        14.40        13.45        45.76        31.04         6.44 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW 
        6.97         3.72         5.29        34.98        36.00        59.01 
TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.96        41.06        45.01         1.74        13.15         2.43 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 
       23.97        12.92         6.97 

$`AMP PEAK  6(1Q44) WILD-TYPE`
TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GM 
      106.88        37.02         3.22       105.37        74.10        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       46.55        38.37        23.21        19.96        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         7.92        91.04 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
        5.33         5.16         7.33         1.18         1.08         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79         0.85         2.40         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE 
        0.76         1.68        14.66        22.49         1.28        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.62         1.94        15.95         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AP-A053 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        2.70         5.95        86.07         8.22        39.42        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM 
       36.89         7.86        12.20        63.16        31.73        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 
       71.67        60.36        49.15         6.71        30.90        27.85 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A062 TCGA-AX-A06D TCGA-AX-A06F 
       19.82        29.69        68.35        45.99        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 
       27.39        30.02        60.66        43.82        40.11        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN TCGA-AX-A1CP 
       19.20        16.96        12.43        20.05        25.12        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       30.12        71.24        61.18        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       26.33        27.32        31.13         0.23         0.10         0.33 
TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU 
        0.20         0.23         8.35        80.38        46.75        48.76 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       44.71        32.55        28.64        30.51        25.91        23.01 
TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       17.85       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       43.96        40.50        16.73        19.56        19.50        18.41 
TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M7 TCGA-BG-A0M9 
       33.11        34.13        34.95        18.61        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0VW 
       10.72        41.52        48.56        23.47        43.30        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A187 
       34.29        52.64        56.58        14.83        12.56        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        15.45        14.27        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A4ZD TCGA-BK-A56F 
       20.12         6.81        34.98         6.21        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        23.47        85.55        78.21 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0UA 
        4.80        77.95        67.99        96.49        97.41        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V6 TCGA-BS-A0V7 
       85.84        82.39        81.57        73.25        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU 
       49.55        66.48        19.79        29.95         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-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       29.88         1.91        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         1.41         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A179 TCGA-D1-A17C TCGA-D1-A17D 
       17.49        19.53         6.64         6.77         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
        1.28        28.01         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-A1O0 
       22.92         1.41        13.22         0.72        18.25         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DG 
       15.06         1.05         3.95         3.52        44.88         4.27 
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        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       24.33        16.01        16.80        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       16.34        14.99        24.36        23.34        23.34        23.90 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A210 
       13.97         6.90        15.81         8.55        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       18.87        22.82        29.10        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        2.14         5.88        40.01        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        96.69         9.07        28.93        25.02        26.01 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT 
       10.82         9.11         7.00        11.24        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                     149.56                      191.84 
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                     20.810                      23.425 
[1] "0.0 - 149.6 (20.8)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.5"
D6V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  6(1Q44) MUTATED                                       148
  AMP PEAK  6(1Q44) WILD-TYPE                                     232
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  6(1Q44) MUTATED                               8
  AMP PEAK  6(1Q44) WILD-TYPE                            13
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  6(1Q44) MUTATED                                  46
  AMP PEAK  6(1Q44) WILD-TYPE                                58
D6V3, multiclass
                                         clus
vv                                        AMP PEAK  6(1Q44) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                       148
  MIXED SEROUS AND ENDOMETRIOID                                   8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              46
                                         clus
vv                                        AMP PEAK  6(1Q44) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         232
  MIXED SEROUS AND ENDOMETRIOID                                    13
  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"
D6V4, binary
                             cls
clus                            0   1
  AMP PEAK  6(1Q44) MUTATED    54 148
  AMP PEAK  6(1Q44) WILD-TYPE  84 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(1Q44) MUTATED     54  148
  AMP PEAK  6(1Q44) WILD-TYPE   84  219
     clus
vv    AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE
  NO                         54                          84
  YES                       148                         219
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  6(1Q44) MUTATED   141  10   9  10
  AMP PEAK  6(1Q44) WILD-TYPE 210  12   8  20
D6V5, multiclass
    clus
vv   AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE
  R0                       141                         210
  R1                        10                          12
  R2                         9                           8
  RX                        10                          20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(1Q44) MUTATED                                  1     5
  AMP PEAK  6(1Q44) WILD-TYPE                                3    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(1Q44) MUTATED                          42
  AMP PEAK  6(1Q44) WILD-TYPE                        48
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(1Q44) MUTATED                                           2   146
  AMP PEAK  6(1Q44) WILD-TYPE                                         7   211
D6V6, multiclass
                                           clus
vv                                          AMP PEAK  6(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                        42
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                           146
                                           clus
vv                                          AMP PEAK  6(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          48
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             211
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                             cls
clus                            0   1
  AMP PEAK  6(1Q44) MUTATED     3 144
  AMP PEAK  6(1Q44) WILD-TYPE  10 206
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(1Q44) MUTATED      3  144
  AMP PEAK  6(1Q44) WILD-TYPE   10  206
                        clus
vv                       AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             3                          10
  NOT HISPANIC OR LATINO                       144                         206
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(2P24.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(2P24.3) MUTATED    87  23
  AMP PEAK  7(2P24.3) WILD-TYPE 356  37
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                          110                           393 
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                           23                            37 
$`AMP PEAK  7(2P24.3) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R6 
      149.56        65.75        60.53        28.27        20.81        19.96 
TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M 
       17.59        36.33        46.32        28.64        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        1.08         0.85         0.49         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05H 
        1.64         0.76        16.87         1.71        39.42        45.53 
TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IU 
       48.79        41.95        18.25        33.73        68.35        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       37.78        16.96        67.50        11.08         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A3FW TCGA-AX-A3G3 
       33.53        68.71        19.36        17.75         0.33         0.03 
TCGA-AX-A3G4 TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11I 
        0.13        43.13        44.71        17.10        11.01        75.72 
TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M6 
       50.89        12.79         5.03        19.33        20.94         7.92 
TCGA-BG-A0M8 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE 
       36.49        15.42        24.39        52.83        15.45        23.70 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE 
       11.31         6.81        35.90        24.13        16.64         4.80 
TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-D1-A0ZO 
       61.87        72.72        73.25        63.58        49.55        19.79 
TCGA-D1-A0ZP TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A17R 
       29.95        36.10        27.42        18.67        28.08        11.15 
TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ 
        8.48         4.11        36.62        35.38        91.96        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GH 
       24.33        18.81        26.96        22.26         6.21        23.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 
        6.90        19.27        15.09         8.55         3.62        14.40 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D2 
       29.10         6.44         3.72         5.88        34.98        36.00 
TCGA-FI-A2D4 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
        7.99        28.93        25.02        41.06        45.01        13.15 
TCGA-PG-A7D5 TCGA-PG-A915 
       23.97         7.00 

$`AMP PEAK  7(2P24.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       46.55        38.37        36.82        23.21        68.65        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60         8.02        91.04         5.33         5.16         7.33 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.97         0.39        19.79         2.40         3.02         1.12 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        2.33         0.99         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       16.24         0.56        13.58        19.82        29.69        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC 
       54.12        25.12        36.39        71.24        61.18        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       40.50        26.33        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 
        0.23         0.10         0.13         0.20        20.52         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        48.76        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 
       30.51        25.91        23.01        17.88        13.74        17.85 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
        4.11         8.71       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 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       21.17        20.28        26.66        16.34        34.29        52.64 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       15.45        14.27         1.81         9.57        35.67        20.12 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        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        23.47        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 
       67.20        88.34        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 
       62.79        63.16        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-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         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         6.77         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-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-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-A2G5 TCGA-D1-A2G7 
       15.06         1.05         3.95         3.52        41.42        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1C3 
        0.26         4.27        27.16        16.31        39.29        24.30 
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        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        6.67        16.01         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 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       27.16        16.34        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       27.16        23.34        23.90        22.78        13.97        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.88        17.62        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33        12.59        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        27.35        13.84        17.92         2.14         6.97 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
        5.29        40.01        33.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 
       59.01         9.07        28.96        26.01         1.74         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       10.82         9.11        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                       149.56                        191.84 
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                       20.875                        23.010 
[1] "0.0 - 149.6 (20.9)" "0.1 - 191.8 (23.0)"
[1] "hr=" "2.4"
D7V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  7(2P24.3) MUTATED                                        53
  AMP PEAK  7(2P24.3) WILD-TYPE                                     327
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  7(2P24.3) MUTATED                               7
  AMP PEAK  7(2P24.3) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  7(2P24.3) MUTATED                                  52
  AMP PEAK  7(2P24.3) WILD-TYPE                                52
D7V3, multiclass
                                         clus
vv                                        AMP PEAK  7(2P24.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          53
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                52
                                         clus
vv                                        AMP PEAK  7(2P24.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           327
  MIXED SEROUS AND ENDOMETRIOID                                      14
  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"
D7V4, binary
                               cls
clus                              0   1
  AMP PEAK  7(2P24.3) MUTATED    22  90
  AMP PEAK  7(2P24.3) WILD-TYPE 116 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(2P24.3) MUTATED     22   90
  AMP PEAK  7(2P24.3) WILD-TYPE  116  277
     clus
vv    AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE
  NO                           22                           116
  YES                          90                           277
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(2P24.3) MUTATED    78   5   5   8
  AMP PEAK  7(2P24.3) WILD-TYPE 273  17  12  22
D7V5, multiclass
    clus
vv   AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE
  R0                          78                           273
  R1                           5                            17
  R2                           5                            12
  RX                           8                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(2P24.3) MUTATED                                  0     3
  AMP PEAK  7(2P24.3) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(2P24.3) MUTATED                          19
  AMP PEAK  7(2P24.3) WILD-TYPE                        71
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(2P24.3) MUTATED                                           4    82
  AMP PEAK  7(2P24.3) WILD-TYPE                                         5   275
D7V6, multiclass
                                           clus
vv                                          AMP PEAK  7(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              82
                                           clus
vv                                          AMP PEAK  7(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               275
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(2P24.3) MUTATED     1  84
  AMP PEAK  7(2P24.3) WILD-TYPE  12 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(2P24.3) MUTATED      1   84
  AMP PEAK  7(2P24.3) WILD-TYPE   12  266
                        clus
vv                       AMP PEAK  7(2P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       AMP PEAK  7(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           266
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(2Q13) MUTATION ANALYSIS
D8V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  8(2Q13) MUTATED    86  22
  AMP PEAK  8(2Q13) WILD-TYPE 357  38
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                        108                         395 
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                         22                          38 
$`AMP PEAK  8(2Q13) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A0GV TCGA-A5-A0R6 TCGA-A5-A0R7 
      149.56        37.02        60.53        20.81        19.96        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       11.44        36.33        28.64        14.96         1.18         1.08 
TCGA-AJ-A3BK TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A05D 
        1.68        22.26         0.92         0.76         1.71        57.80 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       45.53        48.79       125.42        97.71        41.95        18.25 
TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       33.73        68.35        37.78        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G3 
       71.24        61.18        17.75         2.96        38.70         0.03 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K7 
        0.13         0.13        80.38        43.13        23.01        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A3S1 TCGA-B5-A5OD 
       11.01         4.11        75.72        50.89         5.03        34.13 
TCGA-B5-A5OE TCGA-BG-A0M2 TCGA-BG-A0M6 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A2AE 
       34.95        20.94         7.92        15.42        24.39        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
        6.81        35.90        10.22        10.16        24.13        16.64 
TCGA-BS-A0TE TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A168 
        4.80        72.72        63.58        19.79        29.95        36.10 
TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A2G6 
       11.51         6.77        11.15        13.22        18.25         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
       44.88         0.26         4.11        35.38         9.37        91.96 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 
       48.36        24.33        10.92        32.38        19.40        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GJ 
       22.26        16.34         6.21         4.54        23.34        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3QX 
        6.90        19.27        15.09        14.40        29.10        13.84 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2F8 
        6.44         3.72        34.98        36.00         7.99        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       26.01        41.06        45.01        13.15        23.97        12.92 

$`AMP PEAK  8(2Q13) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        36.82        28.27        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         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        7.33         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        3.02         0.49         1.12         0.76         2.24         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87        16.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07         8.22        39.42        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S 
       30.90        10.42        27.85        16.24         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       67.50        25.12        36.39        33.53        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       40.50        19.36        26.33        27.32        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 
        0.10         0.33         0.13         0.20        20.52         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18         8.35        14.47        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F 
       25.91        17.88        13.74        17.85         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        33.11        41.06 
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        34.98        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       15.45        14.27         1.81         9.57        35.67        20.12 
TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       11.31        34.98         6.21        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        23.47        85.55        78.21 
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-A0UV 
       67.20        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        49.55        63.16        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         1.41 
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-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41         0.72        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.01         7.36        16.80        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       35.05        33.01        27.12        57.60        24.79        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G8 TCGA-EY-A1GD 
       19.36        35.15        12.89        27.16        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       24.36        27.16        23.34        22.78        13.97        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        17.62        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59         3.62        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 
       13.45        45.76        31.04        27.35        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D5 
        6.97         5.29         5.88        40.01        33.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
        1.74         2.43        10.82         9.11         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                     149.56                      191.84 
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                     20.385                      23.340 
[1] "0.0 - 149.6 (20.4)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.3"
D8V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  8(2Q13) MUTATED                                        43
  AMP PEAK  8(2Q13) WILD-TYPE                                     337
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  8(2Q13) MUTATED                               5
  AMP PEAK  8(2Q13) WILD-TYPE                            16
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  8(2Q13) MUTATED                                  61
  AMP PEAK  8(2Q13) WILD-TYPE                                43
D8V3, multiclass
                                         clus
vv                                        AMP PEAK  8(2Q13) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        43
  MIXED SEROUS AND ENDOMETRIOID                                   5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              61
                                         clus
vv                                        AMP PEAK  8(2Q13) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         337
  MIXED SEROUS AND ENDOMETRIOID                                    16
  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"
D8V4, binary
                             cls
clus                            0   1
  AMP PEAK  8(2Q13) MUTATED    26  83
  AMP PEAK  8(2Q13) WILD-TYPE 112 284
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(2Q13) MUTATED     26   83
  AMP PEAK  8(2Q13) WILD-TYPE  112  284
     clus
vv    AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE
  NO                         26                         112
  YES                        83                         284
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  8(2Q13) MUTATED    72   5   7   8
  AMP PEAK  8(2Q13) WILD-TYPE 279  17  10  22
D8V5, multiclass
    clus
vv   AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE
  R0                        72                         279
  R1                         5                          17
  R2                         7                          10
  RX                         8                          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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(2Q13) MUTATED                                  0     5
  AMP PEAK  8(2Q13) WILD-TYPE                                4    14
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(2Q13) MUTATED                          27
  AMP PEAK  8(2Q13) WILD-TYPE                        63
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(2Q13) MUTATED                                           2    69
  AMP PEAK  8(2Q13) WILD-TYPE                                         7   288
D8V6, multiclass
                                           clus
vv                                          AMP PEAK  8(2Q13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                        27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            69
                                           clus
vv                                          AMP PEAK  8(2Q13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    4
  ASIAN                                                              14
  BLACK OR AFRICAN AMERICAN                                          63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             288
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                             cls
clus                            0   1
  AMP PEAK  8(2Q13) MUTATED     2  71
  AMP PEAK  8(2Q13) WILD-TYPE  11 279
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(2Q13) MUTATED      2   71
  AMP PEAK  8(2Q13) WILD-TYPE   11  279
                        clus
vv                       AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE
  HISPANIC OR LATINO                             2                          11
  NOT HISPANIC OR LATINO                        71                         279
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(3P25.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(3P25.1) MUTATED    62  15
  AMP PEAK  9(3P25.1) WILD-TYPE 381  45
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           77                           426 
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           15                            45 
$`AMP PEAK  9(3P25.1) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A23N 
       37.02        65.75        36.82        36.33        91.04         1.08 
TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
        0.39         0.85         0.49         0.92         0.76        16.87 
TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LH 
        0.13        39.42        36.89       125.42         3.39        36.36 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A2H2 
       33.40        31.30        68.35        53.92        12.26         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K4 
       30.12        33.53         0.13         0.13        80.38        17.88 
TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A3FB TCGA-B5-A5OE TCGA-BG-A0M4 
       33.50       191.84        11.87        78.81        34.95        34.98 
TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A16S 
       15.42        52.83        67.20        73.25        49.55        18.67 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G6 
        6.77        13.22        18.25         2.07        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
       44.88         4.11        31.10        91.96        48.36        24.33 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU 
       10.92        37.71        24.79        34.39        26.96        22.26 
TCGA-EY-A1GC TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 
        4.54        17.88        17.62        15.09         8.55         3.62 
TCGA-EY-A4KR TCGA-EY-A72D TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
        6.44         5.88        59.01         9.07        25.02        26.01 
TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       45.01        13.15        23.97        12.92         7.00 

$`AMP PEAK  9(3P25.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        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-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.18         1.97        19.79         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         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         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        57.80        45.53         7.86        12.20        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        63.16        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        55.89        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       29.69        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       34.98        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        11.08        71.24        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.03         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       23.01        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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 
       45.90        43.96        40.50        36.82        32.09        27.35 
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-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 
       12.79       116.25        96.30        62.14        33.11         5.03 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21         7.92        38.37        36.49        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       34.29        52.64        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        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        23.47        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        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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 
        1.41         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-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
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         3.52 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 
       24.30        35.38         9.37        12.39        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37         6.67        16.01         7.36        16.80        18.81 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       31.96        35.05        33.01        27.12        57.60        32.38 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW 
       19.40        19.36        35.15        12.89        27.16        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       18.84        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        27.35        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY 
       36.00         7.99        13.84         8.98        96.69        28.93 
TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       28.96        41.06         1.74         2.43        10.82         9.11 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                       191.84                        185.79 
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                       24.330                        22.665 
[1] "0.1 - 191.8 (24.3)" "0.0 - 185.8 (22.7)"
[1] "hr=" "1.8"
D9V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  9(3P25.1) MUTATED                                        34
  AMP PEAK  9(3P25.1) WILD-TYPE                                     346
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK  9(3P25.1) MUTATED                               1
  AMP PEAK  9(3P25.1) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  9(3P25.1) MUTATED                                  43
  AMP PEAK  9(3P25.1) WILD-TYPE                                61
D9V3, multiclass
                                         clus
vv                                        AMP PEAK  9(3P25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          34
  MIXED SEROUS AND ENDOMETRIOID                                     1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                43
                                         clus
vv                                        AMP PEAK  9(3P25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           346
  MIXED SEROUS AND ENDOMETRIOID                                      20
  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"
D9V4, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P25.1) MUTATED    14  64
  AMP PEAK  9(3P25.1) WILD-TYPE 124 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P25.1) MUTATED     14   64
  AMP PEAK  9(3P25.1) WILD-TYPE  124  303
     clus
vv    AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE
  NO                           14                           124
  YES                          64                           303
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(3P25.1) MUTATED    54   3   4   4
  AMP PEAK  9(3P25.1) WILD-TYPE 297  19  13  26
D9V5, multiclass
    clus
vv   AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE
  R0                          54                           297
  R1                           3                            19
  R2                           4                            13
  RX                           4                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(3P25.1) MUTATED                                  0     0
  AMP PEAK  9(3P25.1) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(3P25.1) MUTATED                          21
  AMP PEAK  9(3P25.1) WILD-TYPE                        69
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(3P25.1) MUTATED                                           4    46
  AMP PEAK  9(3P25.1) WILD-TYPE                                         5   311
D9V6, multiclass
                                           clus
vv                                          AMP PEAK  9(3P25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              46
                                           clus
vv                                          AMP PEAK  9(3P25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            69
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P25.1) MUTATED     3  54
  AMP PEAK  9(3P25.1) WILD-TYPE  10 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P25.1) MUTATED      3   54
  AMP PEAK  9(3P25.1) WILD-TYPE   10  296
                        clus
vv                       AMP PEAK  9(3P25.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       AMP PEAK  9(3P25.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           296
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(3P14.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(3P14.1) MUTATED    44  15
  AMP PEAK 10(3P14.1) WILD-TYPE 399  45
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           59                           444 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           15                            45 
$`AMP PEAK 10(3P14.1) MUTATED`
TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EJ 
       19.96        91.04        28.64         0.39         0.49         1.64 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A05D TCGA-AP-A0LO TCGA-AP-A1DO 
       16.87         1.71         0.13        57.80        33.40        31.30 
TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HK TCGA-AX-A2IO 
       68.35        12.26        30.12        33.53         2.96        38.70 
TCGA-AX-A3FW TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A11R 
        0.33         0.13         0.23        23.01        17.88        33.50 
TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A3FB TCGA-B5-A5OD TCGA-BG-A0M4 TCGA-BG-A0RY 
      191.84        11.87        78.81        34.13        34.98        15.42 
TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A16G 
       52.83        12.56        67.20        73.25        49.55        27.42 
TCGA-D1-A179 TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DG 
        6.77         2.07        41.42         8.48        44.88         4.27 
TCGA-D1-A3DH TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A22Y TCGA-EO-A3AZ 
        4.11        12.39        91.96        24.33        24.79        27.16 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 
       26.96         4.54        17.88        15.09         8.55         3.62 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PX 
        5.88        34.98        59.01        26.01        45.01 

$`AMP PEAK 10(3P14.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        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         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
        7.33        14.96         1.18         1.08         1.97        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65         1.35        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       15.95         1.87         2.33         0.99         2.70        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       97.71        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        53.92        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       54.12        67.50        25.12        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        27.32        31.13         0.23         0.10 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.13         0.20        20.52         0.03         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.13        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       30.51        25.91        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        16.73        19.56        19.50        18.41        17.36 
TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       16.57       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD 
       15.29        12.79       116.25        96.30        62.14        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21         7.92        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV 
       39.32        30.81        21.17        20.28        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       16.34        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        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        23.47        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        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A16I 
       36.10        37.32        36.36        37.51        36.79        11.51 
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 
        1.41         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-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        3.95         3.52         0.26        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-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        18.81        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        57.60        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        35.15        12.89        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       31.04        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
        2.14         6.97         3.72         5.29        40.01        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX 
       36.00         7.99        13.84         8.98        96.69         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.93        28.96        25.02        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
        2.43        10.82         9.11        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                       191.84                        185.79 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                       24.330                        22.665 
[1] "0.1 - 191.8 (24.3)" "0.0 - 185.8 (22.7)"
[1] "hr=" "2.6"
D10V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 10(3P14.1) MUTATED                                        31
  AMP PEAK 10(3P14.1) WILD-TYPE                                     349
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 10(3P14.1) MUTATED                               3
  AMP PEAK 10(3P14.1) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 10(3P14.1) MUTATED                                  26
  AMP PEAK 10(3P14.1) WILD-TYPE                                78
D10V3, multiclass
                                         clus
vv                                        AMP PEAK 10(3P14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          31
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                26
                                         clus
vv                                        AMP PEAK 10(3P14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           349
  MIXED SEROUS AND ENDOMETRIOID                                      18
  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"
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     9  51
  AMP PEAK 10(3P14.1) WILD-TYPE 129 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      9   51
  AMP PEAK 10(3P14.1) WILD-TYPE  129  316
     clus
vv    AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  NO                            9                           129
  YES                          51                           316
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(3P14.1) MUTATED    38   5   3   3
  AMP PEAK 10(3P14.1) WILD-TYPE 313  17  14  27
D10V5, multiclass
    clus
vv   AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  R0                          38                           313
  R1                           5                            17
  R2                           3                            14
  RX                           3                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(3P14.1) MUTATED                                  1     0
  AMP PEAK 10(3P14.1) WILD-TYPE                                3    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(3P14.1) MUTATED                          12
  AMP PEAK 10(3P14.1) WILD-TYPE                        78
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(3P14.1) MUTATED                                           4    38
  AMP PEAK 10(3P14.1) WILD-TYPE                                         5   319
D10V6, multiclass
                                           clus
vv                                          AMP PEAK 10(3P14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              38
                                           clus
vv                                          AMP PEAK 10(3P14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            78
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               319
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     4  39
  AMP PEAK 10(3P14.1) WILD-TYPE   9 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      4   39
  AMP PEAK 10(3P14.1) WILD-TYPE    9  311
                        clus
vv                       AMP PEAK 10(3P14.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          39
                        clus
vv                       AMP PEAK 10(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           311
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(3Q26.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(3Q26.2) MUTATED   130  27
  AMP PEAK 11(3Q26.2) WILD-TYPE 313  33
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          157                           346 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                           27                            33 
$`AMP PEAK 11(3Q26.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OK 
       37.02        65.75        36.82        11.44        36.33         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM 
       91.04        46.32        14.96         1.18         1.08         0.85 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        0.49         2.24         1.64        22.26         1.28         0.92 
TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A052 
       15.62        16.87         1.71         0.99         0.13        21.99 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
        5.95        57.80        45.53        36.89        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A5FX 
        3.39        97.71        33.40        31.30        41.95        33.73 
TCGA-AW-A1PO TCGA-AX-A05W TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A0IU TCGA-AX-A0IW 
        0.56        68.35        53.92        12.26        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       16.96        20.28        76.83        36.39        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
       30.12        71.24        33.53        61.18        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
       38.70         0.33         0.13        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JX TCGA-B5-A0K3 TCGA-B5-A0K4 
        0.23         0.13        80.38        44.71        23.01        17.88 
TCGA-B5-A0KB TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY 
        4.11        88.34        75.72        33.50       191.84        11.87 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0M6 
       12.79         5.03        34.13        34.95        34.98         7.92 
TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A3PP 
       36.49        21.17        15.42        52.83        12.56         6.81 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 
       10.22        10.16         4.80        67.20        73.25        49.55 
TCGA-D1-A0ZP TCGA-D1-A15V TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16N TCGA-D1-A16S 
       29.95        39.48        36.10        27.42        31.07        18.67 
TCGA-D1-A176 TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
       30.15         6.77        28.08        13.22         0.72        18.25 
TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH 
        2.07        41.42         8.48        44.88         0.26         4.11 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
       35.38         9.37        31.10        91.96        48.36        24.33 
TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
        7.36        10.92        18.81        37.71        24.79        32.38 
TCGA-EO-A3AS TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ 
       34.39        35.15        26.96        22.26        16.34        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV 
        6.90        19.27        17.88        17.62        15.09        15.81 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX 
        8.55         3.62        14.40        13.45        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        6.44        17.92         3.72         5.88        40.01        34.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       96.69        59.01         9.07        28.93        25.02        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       45.01         1.74        13.15        10.82        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 11(3Q26.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        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         7.92         9.60        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16         7.33         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        3.02         1.12         0.76         1.68        14.66        22.49 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        1.87         2.33         2.70        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
        8.22        39.42         7.86        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       71.67        60.36        55.89        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S 
       30.90        10.42        27.85        16.24        18.25        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       66.58        34.98        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.01        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       67.50        25.12        68.71        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       17.75        27.32        31.13         0.23         0.10         0.20 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       48.76        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       25.91        13.74        17.10        17.85        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      185.79       113.36        54.44        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       36.82        32.09        27.35        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        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        33.11        41.06        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        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        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         6.21        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-A0TG TCGA-BS-A0TI 
       46.95        23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        11.51        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-A177 
        1.41         3.65        17.49        19.53         6.64        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-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        2.33        22.92         1.41        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH 
        1.05         3.95         3.52         4.27        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 
       39.29        36.62        24.30        12.39        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        2.37         6.67        16.01        16.80        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AY 
       33.01        27.12        57.60        19.40        19.36        12.89 
TCGA-EO-A3AZ TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       27.16         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       27.16        23.34        23.34        22.78        13.97        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       16.11        12.43         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A549 
       22.82        45.76        31.04        29.10         2.14         6.97 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.29        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       28.96        26.01         2.43         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                       191.84                        185.79 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                        20.28                         23.36 
[1] "0.0 - 191.8 (20.3)" "0.1 - 185.8 (23.4)"
[1] "hr=" "2"  
D11V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 11(3Q26.2) MUTATED                                        68
  AMP PEAK 11(3Q26.2) WILD-TYPE                                     312
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 11(3Q26.2) MUTATED                               8
  AMP PEAK 11(3Q26.2) WILD-TYPE                            13
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 11(3Q26.2) MUTATED                                  82
  AMP PEAK 11(3Q26.2) WILD-TYPE                                22
D11V3, multiclass
                                         clus
vv                                        AMP PEAK 11(3Q26.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          68
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                82
                                         clus
vv                                        AMP PEAK 11(3Q26.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           312
  MIXED SEROUS AND ENDOMETRIOID                                      13
  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"
D11V4, binary
                               cls
clus                              0   1
  AMP PEAK 11(3Q26.2) MUTATED    35 123
  AMP PEAK 11(3Q26.2) WILD-TYPE 103 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3Q26.2) MUTATED     35  123
  AMP PEAK 11(3Q26.2) WILD-TYPE  103  244
     clus
vv    AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE
  NO                           35                           103
  YES                         123                           244
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(3Q26.2) MUTATED   105   8   9   9
  AMP PEAK 11(3Q26.2) WILD-TYPE 246  14   8  21
D11V5, multiclass
    clus
vv   AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE
  R0                         105                           246
  R1                           8                            14
  R2                           9                             8
  RX                           9                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(3Q26.2) MUTATED                                  0     3
  AMP PEAK 11(3Q26.2) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(3Q26.2) MUTATED                          45
  AMP PEAK 11(3Q26.2) WILD-TYPE                        45
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(3Q26.2) MUTATED                                           4    95
  AMP PEAK 11(3Q26.2) WILD-TYPE                                         5   262
D11V6, multiclass
                                           clus
vv                                          AMP PEAK 11(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          45
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              95
                                           clus
vv                                          AMP PEAK 11(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            45
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               262
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(3Q26.2) MUTATED     3 111
  AMP PEAK 11(3Q26.2) WILD-TYPE  10 239
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3Q26.2) MUTATED      3  111
  AMP PEAK 11(3Q26.2) WILD-TYPE   10  239
                        clus
vv                       AMP PEAK 11(3Q26.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         111
                        clus
vv                       AMP PEAK 11(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           239
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(3Q26.2) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 12(3Q26.2) MUTATED   121  26
  AMP PEAK 12(3Q26.2) WILD-TYPE 322  34
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                          147                           356 
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                           26                            34 
$`AMP PEAK 12(3Q26.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       37.02        65.75        36.82        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD 
       46.32        14.96         1.18         1.08         0.85         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3QS 
        1.12         2.24         1.64        22.26         0.92        16.87 
TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H 
        1.71         0.13        21.99         5.95        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO 
       36.89        48.79       125.42         3.39        97.71        33.40 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05W TCGA-AX-A06D 
       31.30        41.95        33.73         0.56        68.35        12.26 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR 
       37.78        16.96        20.28        76.83        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HF 
        4.77        30.12        71.24        33.53        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
        2.96        38.70         0.33         0.13        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JX TCGA-B5-A0K3 TCGA-B5-A0K4 
        0.13         0.13        80.38        44.71        23.01        17.88 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY 
        4.11         8.71        75.72        33.50       191.84        11.87 
TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 
       12.79        34.13        34.95        34.98         7.92        36.49 
TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC 
       21.17        15.42        52.83        12.56         6.81        10.22 
TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZP 
       10.16         4.80        67.20        73.25        49.55        29.95 
TCGA-D1-A15V TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S 
       39.48        36.10        27.42        11.51        31.07        18.67 
TCGA-D1-A176 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A2G5 
       30.15        28.08        13.22         0.72        18.25        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO 
        8.48        44.88         0.26         4.11        35.38         9.37 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       91.96        48.36        24.33         7.36        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU 
       37.71        24.79        32.38        34.39        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       16.34         4.54        23.90         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 
       17.62        15.09        15.81         8.55         3.62        14.40 
TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A 
       13.45        27.35        13.84         6.44        17.92         3.72 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        5.88        40.01        34.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A5BC 
       28.93        25.02        41.06        45.01        13.15        10.82 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       23.97        12.92         7.00 

$`AMP PEAK 12(3Q26.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K4 
       42.35        15.95         7.92         9.60         8.02        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.33         5.16         7.33         1.97         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40         3.02         0.76         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        1.28        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.94        15.95         1.87         2.33         0.99         2.70 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
       83.67        23.31        86.07         8.22        39.42         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20        20.91       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       16.24        18.25        13.58        19.82        29.69        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       25.12        68.71        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G7 
       27.32        31.13         0.23         0.10         0.20         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       48.76        40.67        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       25.91        13.74        17.10        17.85        11.01       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       36.82        32.09        27.35        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        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11         5.03        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        38.37        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       30.81        20.28        24.39        26.66        16.34        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-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
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         6.21 
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-A0TG 
        9.86        46.95        23.47        85.55        78.21        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        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       63.58        63.16        66.48        16.83        19.79         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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        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-A177 
        1.41         3.65        17.49        19.53         6.64        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
        6.77         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-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG 
        2.07        15.06         1.05         3.95         3.52         4.27 
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-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G7 
       19.40        19.36        35.15        12.89        27.16         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       22.78        13.97        18.84        16.11        12.43         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        18.87        22.82        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 
       29.10         2.14         6.97         5.29        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR 
        7.99        13.84         8.98        28.96        26.01         1.74 
TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        2.43         9.11        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                       191.84                        185.79 
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                        20.28                         23.36 
[1] "0.0 - 191.8 (20.3)" "0.1 - 185.8 (23.4)"
[1] "hr=" "2"  
D12V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 12(3Q26.2) MUTATED                                        61
  AMP PEAK 12(3Q26.2) WILD-TYPE                                     319
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 12(3Q26.2) MUTATED                               7
  AMP PEAK 12(3Q26.2) WILD-TYPE                            14
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 12(3Q26.2) MUTATED                                  80
  AMP PEAK 12(3Q26.2) WILD-TYPE                                24
D12V3, multiclass
                                         clus
vv                                        AMP PEAK 12(3Q26.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          61
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                80
                                         clus
vv                                        AMP PEAK 12(3Q26.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           319
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                               cls
clus                              0   1
  AMP PEAK 12(3Q26.2) MUTATED    33 115
  AMP PEAK 12(3Q26.2) WILD-TYPE 105 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(3Q26.2) MUTATED     33  115
  AMP PEAK 12(3Q26.2) WILD-TYPE  105  252
     clus
vv    AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE
  NO                           33                           105
  YES                         115                           252
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(3Q26.2) MUTATED    98   8   9   8
  AMP PEAK 12(3Q26.2) WILD-TYPE 253  14   8  22
D12V5, multiclass
    clus
vv   AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE
  R0                          98                           253
  R1                           8                            14
  R2                           9                             8
  RX                           8                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(3Q26.2) MUTATED                                  0     3
  AMP PEAK 12(3Q26.2) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(3Q26.2) MUTATED                          42
  AMP PEAK 12(3Q26.2) WILD-TYPE                        48
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(3Q26.2) MUTATED                                           4    89
  AMP PEAK 12(3Q26.2) WILD-TYPE                                         5   268
D12V6, multiclass
                                           clus
vv                                          AMP PEAK 12(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          42
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              89
                                           clus
vv                                          AMP PEAK 12(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            48
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               268
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(3Q26.2) MUTATED     2 104
  AMP PEAK 12(3Q26.2) WILD-TYPE  11 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(3Q26.2) MUTATED      2  104
  AMP PEAK 12(3Q26.2) WILD-TYPE   11  246
                        clus
vv                       AMP PEAK 12(3Q26.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         104
                        clus
vv                       AMP PEAK 12(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           246
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(4P16.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 13(4P16.3) MUTATED    43   8
  AMP PEAK 13(4P16.3) WILD-TYPE 400  52
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           51                           452 
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                            8                            52 
$`AMP PEAK 13(4P16.3) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QM 
       37.02        11.44        91.04         1.18         1.08         0.85 
TCGA-AJ-A3BF TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
        1.12        39.42        36.89        48.79       125.42        97.71 
TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 
       28.54        16.96        76.83        25.12         4.77        71.24 
TCGA-AX-A2HH TCGA-AX-A3FW TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A3S1 TCGA-B5-A5OD 
       17.75         0.33         0.03        80.38         5.03        34.13 
TCGA-BG-A0M6 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A16I 
        7.92        10.22        10.16        16.64        22.55        11.51 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH 
       31.07        18.67        18.25         2.07        44.88         4.11 
TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       91.96        10.92        37.71        32.38        19.40        34.39 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A72D 
       26.96        16.34        23.90         8.55        29.10         5.88 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-PG-A914 
       96.69        26.01        12.92 

$`AMP PEAK 13(4P16.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        7.33        14.96         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         0.49         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.87        16.87         1.71         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        57.80        45.53         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW 
       51.09        27.39        30.02        60.66        35.01        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        36.39        11.08        30.12        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       68.71        33.40        40.50        19.36        26.33        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX 
        2.96        31.13        38.70         0.23         0.10         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.13        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        33.11        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-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
        6.81        35.90        34.98         6.21        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        23.47 
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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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         1.41         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         6.77 
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-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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH 
       41.42         8.48         0.26         4.27        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-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
       24.33        16.01         7.36        16.80        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       35.05        33.01        27.12        57.60        24.79        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        27.16        22.26         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       13.45        45.76        31.04        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       45.01         1.74        13.15         2.43        10.82         9.11 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.97         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                       19.400                        22.965 
[1] "0.0 - 125.4 (19.4)" "0.1 - 191.8 (23.0)"
[1] "hr=" "1.4"
D13V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 13(4P16.3) MUTATED                                        15
  AMP PEAK 13(4P16.3) WILD-TYPE                                     365
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 13(4P16.3) MUTATED                               1
  AMP PEAK 13(4P16.3) WILD-TYPE                            20
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 13(4P16.3) MUTATED                                  35
  AMP PEAK 13(4P16.3) WILD-TYPE                                69
D13V3, multiclass
                                         clus
vv                                        AMP PEAK 13(4P16.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          15
  MIXED SEROUS AND ENDOMETRIOID                                     1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                35
                                         clus
vv                                        AMP PEAK 13(4P16.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           365
  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"
D13V4, binary
                               cls
clus                              0   1
  AMP PEAK 13(4P16.3) MUTATED    15  36
  AMP PEAK 13(4P16.3) WILD-TYPE 123 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4P16.3) MUTATED     15   36
  AMP PEAK 13(4P16.3) WILD-TYPE  123  331
     clus
vv    AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE
  NO                           15                           123
  YES                          36                           331
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(4P16.3) MUTATED    34   3   4   2
  AMP PEAK 13(4P16.3) WILD-TYPE 317  19  13  28
D13V5, multiclass
    clus
vv   AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE
  R0                          34                           317
  R1                           3                            19
  R2                           4                            13
  RX                           2                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(4P16.3) MUTATED                                  0     2
  AMP PEAK 13(4P16.3) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(4P16.3) MUTATED                          13
  AMP PEAK 13(4P16.3) WILD-TYPE                        77
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(4P16.3) MUTATED                                           0    29
  AMP PEAK 13(4P16.3) WILD-TYPE                                         9   328
D13V6, multiclass
                                           clus
vv                                          AMP PEAK 13(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              29
                                           clus
vv                                          AMP PEAK 13(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            77
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               328
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                               cls
clus                              0   1
  AMP PEAK 13(4P16.3) MUTATED     2  31
  AMP PEAK 13(4P16.3) WILD-TYPE  11 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4P16.3) MUTATED      2   31
  AMP PEAK 13(4P16.3) WILD-TYPE   11  319
                        clus
vv                       AMP PEAK 13(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          31
                        clus
vv                       AMP PEAK 13(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           319
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(5P15.33) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(5P15.33) MUTATED    66  17
  AMP PEAK 14(5P15.33) WILD-TYPE 377  43
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            83                            420 
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            17                             43 
$`AMP PEAK 14(5P15.33) MUTATED`
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         1.08 
TCGA-AJ-A2QK TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.39        22.26         0.92         0.76        16.87         1.71 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DO 
       45.53        48.79       125.42        36.36        97.71        31.30 
TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A2H2 TCGA-AX-A2H5 
       41.95         0.56        35.01        37.78         4.77        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
       61.18         2.96         0.20        20.52         0.03         0.13 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE 
        0.13        80.38        11.87        33.11        34.13        34.95 
TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC 
       35.21         7.92        24.39        15.45         6.81        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A16N 
       10.16        24.13         4.80        49.55        39.48        31.07 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH TCGA-DI-A1NN 
        6.77        13.22         0.72        18.25         4.11        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
        9.37        12.39        31.10        91.96        48.36        24.33 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC 
       10.92        37.71        32.38        26.96        22.26         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3QX TCGA-EY-A4KR 
       23.90        17.62        15.09        13.45        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       17.92         5.88        36.00        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A914 TCGA-PG-A915 
       25.02         1.74        13.15        12.92         7.00 

$`AMP PEAK 14(5P15.33) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GD 
        1.08       106.88       149.56        83.51        17.85         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        87.32        74.10        57.53        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        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-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.18         1.97        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.49         1.12         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.62         1.94        15.95         1.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        18.25        33.73        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       25.12        36.39        11.08        30.12        33.53        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.23         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 
       12.79       116.25        96.30        78.81        62.14         5.03 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       41.06        18.61        20.19        19.33        20.94        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
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         6.21 
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        23.47        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        67.20        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-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 
        1.41         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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ 
       41.42         8.48        44.88         0.26         4.27        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1LX TCGA-E6-A1M0 
       16.31        39.29        36.62        24.30        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37         6.67        16.01         7.36        16.80        18.81 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.88        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59         3.62        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A548 
       22.82        45.76        31.04        29.10        27.35         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F9 
        7.99        13.84         8.98        96.69        28.96        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       41.06        45.01         2.43        10.82         9.11        23.97 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                        125.42                         191.84 
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                         18.25                          23.26 
[1] "0.0 - 125.4 (18.2)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.3"
D14V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 14(5P15.33) MUTATED                                        28
  AMP PEAK 14(5P15.33) WILD-TYPE                                     352
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 14(5P15.33) MUTATED                               3
  AMP PEAK 14(5P15.33) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 14(5P15.33) MUTATED                                  52
  AMP PEAK 14(5P15.33) WILD-TYPE                                52
D14V3, multiclass
                                         clus
vv                                        AMP PEAK 14(5P15.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           28
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 52
                                         clus
vv                                        AMP PEAK 14(5P15.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            352
  MIXED SEROUS AND ENDOMETRIOID                                       18
  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"
D14V4, binary
                                cls
clus                               0   1
  AMP PEAK 14(5P15.33) MUTATED    17  66
  AMP PEAK 14(5P15.33) WILD-TYPE 121 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(5P15.33) MUTATED     17   66
  AMP PEAK 14(5P15.33) WILD-TYPE  121  301
     clus
vv    AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE
  NO                            17                            121
  YES                           66                            301
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(5P15.33) MUTATED    56   3   6   7
  AMP PEAK 14(5P15.33) WILD-TYPE 295  19  11  23
D14V5, multiclass
    clus
vv   AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE
  R0                           56                            295
  R1                            3                             19
  R2                            6                             11
  RX                            7                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(5P15.33) MUTATED                                  1     2
  AMP PEAK 14(5P15.33) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(5P15.33) MUTATED                          27
  AMP PEAK 14(5P15.33) WILD-TYPE                        63
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 14(5P15.33) MUTATED                                           2
  AMP PEAK 14(5P15.33) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 14(5P15.33) MUTATED      47
  AMP PEAK 14(5P15.33) WILD-TYPE   310
D14V6, multiclass
                                           clus
vv                                          AMP PEAK 14(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               47
                                           clus
vv                                          AMP PEAK 14(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                310
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(5P15.33) MUTATED     4  57
  AMP PEAK 14(5P15.33) WILD-TYPE   9 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(5P15.33) MUTATED      4   57
  AMP PEAK 14(5P15.33) WILD-TYPE    9  293
                        clus
vv                       AMP PEAK 14(5P15.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       AMP PEAK 14(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            293
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(5Q35.3) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 15(5Q35.3) MUTATED    42   8
  AMP PEAK 15(5Q35.3) WILD-TYPE 401  52
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           50                           453 
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                            8                            52 
$`AMP PEAK 15(5Q35.3) MUTATED`
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A6NU 
        1.08         0.85         1.12         0.76        16.87         0.99 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A1DO TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IS 
        5.95        57.80        31.30        18.25        53.92        35.01 
TCGA-AX-A1C8 TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A3FW TCGA-AX-A3G1 
       13.55         4.77        71.24        61.18         0.33        20.52 
TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M6 
        0.03         0.13        80.38        11.87        12.79         7.92 
TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0TI TCGA-D1-A16G 
       24.39        15.45         6.81         4.80        61.87        27.42 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-DI-A1NN TCGA-E6-A1LZ 
        0.72        18.25         2.07         4.27        35.38        48.36 
TCGA-EO-A1Y5 TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A3L3 
       10.92        17.62        15.09        12.59        29.10        27.35 
TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-K6-A3WQ 
        3.72        96.69        59.01        26.01         1.74        13.15 
TCGA-PG-A7D5 TCGA-PG-A914 
       23.97        12.92 

$`AMP PEAK 15(5Q35.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       28.64         5.33         5.16         7.33        14.96         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        1.97         0.39        19.79         2.40         3.02         0.49 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87         1.71         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ 
       25.08        71.67        60.36        55.89        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IU 
       12.26        51.09        27.39        30.02        60.66        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       30.12        33.53        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.23         0.10         0.13         0.20         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        14.40        14.70        11.70        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        38.37        36.49        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        21.17        20.28        15.42        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        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         6.21        10.22        10.16        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-A0TJ TCGA-BS-A0U5 
       23.47        85.55        78.21        77.95        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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A16I 
       36.10        37.32        36.36        37.51        36.79        11.51 
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 
        1.41         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         6.77         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-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       13.22        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH 
        3.52        41.42         8.48        44.88         0.26         4.11 
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        91.96        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        6.67        24.33        16.01         7.36        16.80        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       12.89        27.16        26.96        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.88        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        45.76        31.04        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX 
       33.99        36.00         7.99        13.84         8.98         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 
       28.93        28.96        25.02        41.06        45.01         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       10.82         9.11         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                        96.69                        191.84 
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                        14.32                         23.38 
[1] "0.0 - 96.7 (14.3)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "1.9"
D15V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 15(5Q35.3) MUTATED                                        19
  AMP PEAK 15(5Q35.3) WILD-TYPE                                     361
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 15(5Q35.3) MUTATED                               2
  AMP PEAK 15(5Q35.3) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 15(5Q35.3) MUTATED                                  29
  AMP PEAK 15(5Q35.3) WILD-TYPE                                75
D15V3, multiclass
                                         clus
vv                                        AMP PEAK 15(5Q35.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          19
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                29
                                         clus
vv                                        AMP PEAK 15(5Q35.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           361
  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"
D15V4, binary
                               cls
clus                              0   1
  AMP PEAK 15(5Q35.3) MUTATED     9  41
  AMP PEAK 15(5Q35.3) WILD-TYPE 129 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5Q35.3) MUTATED      9   41
  AMP PEAK 15(5Q35.3) WILD-TYPE  129  326
     clus
vv    AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE
  NO                            9                           129
  YES                          41                           326
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(5Q35.3) MUTATED    32   3   3   3
  AMP PEAK 15(5Q35.3) WILD-TYPE 319  19  14  27
D15V5, multiclass
    clus
vv   AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE
  R0                          32                           319
  R1                           3                            19
  R2                           3                            14
  RX                           3                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(5Q35.3) MUTATED                                  0     1
  AMP PEAK 15(5Q35.3) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(5Q35.3) MUTATED                          18
  AMP PEAK 15(5Q35.3) WILD-TYPE                        72
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 15(5Q35.3) MUTATED                                           0    29
  AMP PEAK 15(5Q35.3) WILD-TYPE                                         9   328
D15V6, multiclass
                                           clus
vv                                          AMP PEAK 15(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              29
                                           clus
vv                                          AMP PEAK 15(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               328
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                              0   1
  AMP PEAK 15(5Q35.3) MUTATED     0  42
  AMP PEAK 15(5Q35.3) WILD-TYPE  13 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5Q35.3) MUTATED      0   42
  AMP PEAK 15(5Q35.3) WILD-TYPE   13  308
                        clus
vv                       AMP PEAK 15(5Q35.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       AMP PEAK 15(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           308
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(6P24.2) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 16(6P24.2) MUTATED    92  16
  AMP PEAK 16(6P24.2) WILD-TYPE 351  44
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                          108                           395 
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                           16                            44 
$`AMP PEAK 16(6P24.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP 
       37.02        36.82        11.44        36.33        91.04        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        1.18         1.08         0.49         1.12         2.24         1.64 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A053 
        0.92         0.76        16.87         1.71         0.13         5.95 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       39.42        57.80        45.53        48.79       125.42        97.71 
TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A06J TCGA-AX-A0IW 
       33.40        41.95        33.73        53.92        30.02        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 
       16.96        20.28        12.43        76.83        11.08        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
       33.53        68.71        38.70         0.13        20.52         0.03 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11E 
        0.13        80.38        46.75        23.01        17.85         8.71 
TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FB 
       75.72        33.50        27.35        50.89        12.79        78.81 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 
        5.03        34.13        34.95        36.49        15.45        35.90 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 
       10.22        24.13        16.64        67.20        49.55        36.10 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G5 
       31.07        18.67         6.77         0.72         2.07        41.42 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A8L9 
        4.27         4.11        35.38        31.10        91.96        24.33 
TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       37.71        24.79        32.38        26.96        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A212 TCGA-EY-A214 
        4.54        19.27        17.88        17.62         3.62        14.40 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CX TCGA-FI-A2D0 
       13.45        29.10        27.35        13.84        40.01        33.99 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       36.00        96.69        59.01         9.07        28.93        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.01        45.01        13.15        23.97        12.92         7.00 

$`AMP PEAK 16(6P24.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O 
       46.32        28.64         5.33         5.16         7.33         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79         0.85         2.40         3.02         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68        14.66        22.49        22.26         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        2.33         0.99         2.70        83.67        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        36.89         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        18.25         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS 
       34.98        12.26        51.09        27.39        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       13.55        15.25        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC 
       25.12        36.39         4.77        71.24        61.18        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 
       31.13         0.23         0.10         0.33         0.20         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JT 
        0.23         1.18         8.35        14.47        56.91        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        4.11       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V 
       43.96        40.50        36.82        32.09        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       191.84       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       14.40        14.70        11.70        11.87        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       96.30        62.14        33.11        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31         6.81        34.98         6.21        10.16 
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-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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         1.41         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-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        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         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       44.88         0.26        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30         9.37        12.39        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       18.81        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        18.87        22.82        45.76        31.04 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 
        5.88        34.98         7.99        13.84         8.98        28.96 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 
       41.06         1.74         2.43        10.82         9.11        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                       24.905                        21.990 
[1] "0.0 - 125.4 (24.9)" "0.1 - 191.8 (22.0)"
[1] "hr=" "1.3"
D16V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 16(6P24.2) MUTATED                                        42
  AMP PEAK 16(6P24.2) WILD-TYPE                                     338
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 16(6P24.2) MUTATED                               5
  AMP PEAK 16(6P24.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 16(6P24.2) MUTATED                                  62
  AMP PEAK 16(6P24.2) WILD-TYPE                                42
D16V3, multiclass
                                         clus
vv                                        AMP PEAK 16(6P24.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          42
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                62
                                         clus
vv                                        AMP PEAK 16(6P24.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           338
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D16V4, binary
                               cls
clus                              0   1
  AMP PEAK 16(6P24.2) MUTATED    22  87
  AMP PEAK 16(6P24.2) WILD-TYPE 116 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(6P24.2) MUTATED     22   87
  AMP PEAK 16(6P24.2) WILD-TYPE  116  280
     clus
vv    AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE
  NO                           22                           116
  YES                          87                           280
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(6P24.2) MUTATED    72   4   5   7
  AMP PEAK 16(6P24.2) WILD-TYPE 279  18  12  23
D16V5, multiclass
    clus
vv   AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE
  R0                          72                           279
  R1                           4                            18
  R2                           5                            12
  RX                           7                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(6P24.2) MUTATED                                  0     2
  AMP PEAK 16(6P24.2) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(6P24.2) MUTATED                          27
  AMP PEAK 16(6P24.2) WILD-TYPE                        63
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(6P24.2) MUTATED                                           2    72
  AMP PEAK 16(6P24.2) WILD-TYPE                                         7   285
D16V6, multiclass
                                           clus
vv                                          AMP PEAK 16(6P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              72
                                           clus
vv                                          AMP PEAK 16(6P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               285
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(6P24.2) MUTATED     2  71
  AMP PEAK 16(6P24.2) WILD-TYPE  11 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(6P24.2) MUTATED      2   71
  AMP PEAK 16(6P24.2) WILD-TYPE   11  279
                        clus
vv                       AMP PEAK 16(6P24.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       AMP PEAK 16(6P24.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           279
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(6P22.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 17(6P22.3) MUTATED    86  11
  AMP PEAK 17(6P22.3) WILD-TYPE 357  49
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                           97                           406 
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                           11                            49 
$`AMP PEAK 17(6P22.3) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23M 
       37.02        11.44        36.33        91.04        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A3NH 
        1.08         0.49         1.12         2.24         0.92         0.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A05D TCGA-AP-A0L8 
       16.87         1.71         0.99         0.13        57.80        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J 
      125.42        97.71        33.40        41.95        33.73        30.02 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR 
       37.78        16.96        20.28        12.43        76.83        11.08 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN 
       33.53        68.71        20.52         0.03         0.13        80.38 
TCGA-B5-A0JS TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R 
       46.75        17.85         4.11         8.71        75.72        33.50 
TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       27.35        50.89        12.79         5.03        34.13        34.95 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD 
       36.49        15.45        35.90        10.22        24.13        16.64 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU 
       67.20        49.55        36.10        31.07        18.67        13.22 
TCGA-D1-A1NW TCGA-D1-A2G5 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO 
        0.72        41.42         4.27         4.11        35.38         9.37 
TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 
       91.96        24.33        37.71        24.79        32.38        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR 
       22.26        16.34         4.54        19.27        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ 
       15.09        12.59         3.62        14.40        13.45        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EX 
       27.35        13.84        40.01        33.99        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       28.93        26.01        45.01        13.15        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 17(6P22.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        46.32        28.64         5.33         5.16         7.33 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76         1.68         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 
        1.28        36.99        20.65         1.35        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 
       15.95         1.87         2.33         2.70        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        5.95        23.31        86.07         8.22        39.42        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        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        30.90        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       12.26        51.09        27.39        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       15.25        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC 
       36.39         4.77        30.12        71.24        61.18        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.13         0.23         1.18         8.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       13.74        17.10        11.01       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        45.90        43.96        40.50        36.82        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 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       15.29       116.25        96.30        78.81        62.14        33.11 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98         7.92        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
       34.98         6.21        10.16        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        23.47        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        88.34        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        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         1.41         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         6.77         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         3.52         8.48        44.88         0.26 
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-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.01         7.36        16.80        10.92        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS 
       35.05        33.01        27.12        57.60        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G7 TCGA-EY-A1G8 
       19.36        35.15        12.89        27.16         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       22.78        13.97         6.90        18.84        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81         8.55         6.48        19.33        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 
        3.72         5.29         5.88        34.98        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       13.84         8.98        96.69        28.96        25.02        41.06 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        1.74         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                       20.520                        22.965 
[1] "0.0 - 125.4 (20.5)" "0.1 - 191.8 (23.0)"
[1] "hr=" "1"  
D17V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 17(6P22.3) MUTATED                                        37
  AMP PEAK 17(6P22.3) WILD-TYPE                                     343
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 17(6P22.3) MUTATED                               4
  AMP PEAK 17(6P22.3) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 17(6P22.3) MUTATED                                  57
  AMP PEAK 17(6P22.3) WILD-TYPE                                47
D17V3, multiclass
                                         clus
vv                                        AMP PEAK 17(6P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          37
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                57
                                         clus
vv                                        AMP PEAK 17(6P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           343
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                               cls
clus                              0   1
  AMP PEAK 17(6P22.3) MUTATED    20  78
  AMP PEAK 17(6P22.3) WILD-TYPE 118 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(6P22.3) MUTATED     20   78
  AMP PEAK 17(6P22.3) WILD-TYPE  118  289
     clus
vv    AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE
  NO                           20                           118
  YES                          78                           289
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(6P22.3) MUTATED    64   3   5   7
  AMP PEAK 17(6P22.3) WILD-TYPE 287  19  12  23
D17V5, multiclass
    clus
vv   AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE
  R0                          64                           287
  R1                           3                            19
  R2                           5                            12
  RX                           7                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(6P22.3) MUTATED                                  0     2
  AMP PEAK 17(6P22.3) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(6P22.3) MUTATED                          29
  AMP PEAK 17(6P22.3) WILD-TYPE                        61
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 17(6P22.3) MUTATED                                           2    60
  AMP PEAK 17(6P22.3) WILD-TYPE                                         7   297
D17V6, multiclass
                                           clus
vv                                          AMP PEAK 17(6P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              60
                                           clus
vv                                          AMP PEAK 17(6P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               297
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(6P22.3) MUTATED     1  65
  AMP PEAK 17(6P22.3) WILD-TYPE  12 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(6P22.3) MUTATED      1   65
  AMP PEAK 17(6P22.3) WILD-TYPE   12  285
                        clus
vv                       AMP PEAK 17(6P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          65
                        clus
vv                       AMP PEAK 17(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           285
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(6Q25.1) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 18(6Q25.1) MUTATED    69  11
  AMP PEAK 18(6Q25.1) WILD-TYPE 374  49
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           80                           423 
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           11                            49 
$`AMP PEAK 18(6Q25.1) MUTATED`
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3IA 
       14.96         1.18         2.40         2.24        22.26         0.92 
TCGA-AJ-A3NH TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ 
        0.76         0.13        48.79        97.71        33.40        41.95 
TCGA-AP-A5FX TCGA-AX-A06J TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       33.73        30.02        12.43        30.12        33.53        68.71 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
        0.33         0.13        20.52         0.13        80.38        23.01 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A1N2 
       17.85         4.11         8.71        75.72        33.50        12.79 
TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 
       78.81         5.03        34.13        36.49        15.45        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
       10.22        10.16        24.13        16.64        61.87        67.20 
TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K 
       49.55         8.55        36.10        11.51        18.67        28.08 
TCGA-D1-A2G5 TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22X TCGA-EO-A22Y 
       41.42        35.38        10.92        18.81        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GO 
       32.38        22.26        16.34         4.54        23.90        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 
       17.88        17.62        15.09        15.81         3.62        14.40 
TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX 
       13.45        27.35        13.84         6.44         3.72        40.01 
TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       33.99        59.01         9.07        25.02        26.01        45.01 
TCGA-PG-A5BC TCGA-PG-A915 
       10.82         7.00 

$`AMP PEAK 18(6Q25.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A23O 
       28.64         5.33         5.16         7.33         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
        0.39        19.79         0.85         3.02         0.49         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        0.76         1.68         1.64        14.66        22.49         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.87        16.87         1.71         2.33         0.99         2.70 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       36.36        31.73        83.97        27.12        82.52        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
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        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        18.25         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08         4.77        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       17.88        13.74        17.10        11.01       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       32.09        27.35        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       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        11.87        15.29       116.25        96.30 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       20.12        11.31         6.81        34.98         6.21        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        23.47 
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        88.34        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        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79        29.95         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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         1.41         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         6.77         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-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         3.52         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26         4.27         4.11        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        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.01         7.36        16.80        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       33.01        27.12        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       12.89        27.16        26.96         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
        6.90        18.84        16.11        12.43         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        18.87        22.82        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       29.10        17.92         2.14         6.97         5.29         5.88 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.93        28.96        41.06         1.74        13.15         2.43 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                         0.13                          0.03 
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                        97.71                        191.84 
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                        19.04                         23.34 
[1] "0.1 - 97.7 (19.0)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "1.4"
D18V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 18(6Q25.1) MUTATED                                        42
  AMP PEAK 18(6Q25.1) WILD-TYPE                                     338
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 18(6Q25.1) MUTATED                               2
  AMP PEAK 18(6Q25.1) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 18(6Q25.1) MUTATED                                  36
  AMP PEAK 18(6Q25.1) WILD-TYPE                                68
D18V3, multiclass
                                         clus
vv                                        AMP PEAK 18(6Q25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          42
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                36
                                         clus
vv                                        AMP PEAK 18(6Q25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           338
  MIXED SEROUS AND ENDOMETRIOID                                      19
  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"
D18V4, binary
                               cls
clus                              0   1
  AMP PEAK 18(6Q25.1) MUTATED    18  62
  AMP PEAK 18(6Q25.1) WILD-TYPE 120 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(6Q25.1) MUTATED     18   62
  AMP PEAK 18(6Q25.1) WILD-TYPE  120  305
     clus
vv    AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE
  NO                           18                           120
  YES                          62                           305
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(6Q25.1) MUTATED    52   1   4   6
  AMP PEAK 18(6Q25.1) WILD-TYPE 299  21  13  24
D18V5, multiclass
    clus
vv   AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE
  R0                          52                           299
  R1                           1                            21
  R2                           4                            13
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(6Q25.1) MUTATED                                  0     1
  AMP PEAK 18(6Q25.1) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(6Q25.1) MUTATED                          25
  AMP PEAK 18(6Q25.1) WILD-TYPE                        65
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(6Q25.1) MUTATED                                           2    46
  AMP PEAK 18(6Q25.1) WILD-TYPE                                         7   311
D18V6, multiclass
                                           clus
vv                                          AMP PEAK 18(6Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              46
                                           clus
vv                                          AMP PEAK 18(6Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(6Q25.1) MUTATED     1  52
  AMP PEAK 18(6Q25.1) WILD-TYPE  12 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(6Q25.1) MUTATED      1   52
  AMP PEAK 18(6Q25.1) WILD-TYPE   12  298
                        clus
vv                       AMP PEAK 18(6Q25.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          52
                        clus
vv                       AMP PEAK 18(6Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           298
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(7Q31.2) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 19(7Q31.2) MUTATED    60  21
  AMP PEAK 19(7Q31.2) WILD-TYPE 383  39
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           81                           422 
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           21                            39 
$`AMP PEAK 19(7Q31.2) MUTATED`
TCGA-A5-A0GV TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A2QN TCGA-AJ-A3BF 
       20.81        36.33        28.64        14.96         2.40         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW 
        2.24         1.64         0.92        15.62        16.87         1.71 
TCGA-AJ-A6NU TCGA-AP-A053 TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LH 
        0.99         5.95        48.79       125.42         3.39        36.36 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A1C8 TCGA-AX-A1C9 
       97.71        33.40        18.25        68.35        13.55        15.25 
TCGA-AX-A2H4 TCGA-AX-A2HJ TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3GI 
       30.12        27.32         0.20        20.52         0.03         0.13 
TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0KB TCGA-B5-A1MS 
       56.91        43.13        28.34        17.88         4.11       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-BG-A0M3 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0RY 
       50.89        14.40        35.21        36.49        30.81        15.42 
TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 TCGA-BK-A4ZD TCGA-BS-A0TE 
       24.39        15.45        23.70        35.90        16.64         4.80 
TCGA-BS-A0TI TCGA-BS-A0UT TCGA-D1-A0ZN TCGA-D1-A16I TCGA-D1-A17C TCGA-D1-A17R 
       61.87        72.72        16.83        11.51         0.99        11.15 
TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A8L9 
        0.72        16.87         8.48         9.37        31.10        24.33 
TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GL 
       16.01        37.71        24.79         6.21        23.34        13.97 
TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A4KR 
       19.27         8.55         6.48         3.62        14.40         6.44 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX 
        6.97         5.88        36.00         9.07        28.93        45.01 
TCGA-K6-A3WQ TCGA-PG-A915 TCGA-QS-A5YQ 
       13.15         7.00         4.21 

$`AMP PEAK 19(7Q31.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        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        19.96        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33         1.18         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        0.85         3.02         0.49         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT 
        0.76         1.94        15.95         1.87         2.33         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        0.13        83.67        21.99        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
       20.91       117.99       110.37        63.16        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        16.96        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08         4.77        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HK 
       33.40        40.50        19.36        26.33        17.75         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN 
        0.13         0.23         1.18         8.35        14.47        80.38 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        23.01        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
       17.36        16.57       191.84        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       33.11         5.03        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       20.19        19.33        20.94        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        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        39.32        21.17        20.28        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA 
        9.57        35.67        20.12        11.31         6.81        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
        6.21        10.22        10.16        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        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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         1.41         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         6.77         1.58         7.00 
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-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-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       13.22        18.25        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       35.38        12.39        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        2.37         6.67         7.36        16.80        10.92        18.81 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       31.96        35.05        33.01        27.12        57.60        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        22.26        16.34        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GM 
       24.36        27.16        23.34        23.90        22.78         6.90 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       15.81        19.33        12.59        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       45.76        31.04        29.10        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        59.01        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC 
       25.02        26.01        41.06         1.74         2.43        10.82 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YR 
       39.95         5.52 

  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                       16.010                        23.915 
[1] "0.0 - 125.4 (16.0)" "0.1 - 191.8 (23.9)"
[1] "hr=" "3.6"
D19V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 19(7Q31.2) MUTATED                                        49
  AMP PEAK 19(7Q31.2) WILD-TYPE                                     331
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 19(7Q31.2) MUTATED                               5
  AMP PEAK 19(7Q31.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 19(7Q31.2) MUTATED                                  28
  AMP PEAK 19(7Q31.2) WILD-TYPE                                76
D19V3, multiclass
                                         clus
vv                                        AMP PEAK 19(7Q31.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          49
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                28
                                         clus
vv                                        AMP PEAK 19(7Q31.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           331
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                               cls
clus                              0   1
  AMP PEAK 19(7Q31.2) MUTATED    14  68
  AMP PEAK 19(7Q31.2) WILD-TYPE 124 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(7Q31.2) MUTATED     14   68
  AMP PEAK 19(7Q31.2) WILD-TYPE  124  299
     clus
vv    AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE
  NO                           14                           124
  YES                          68                           299
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 19(7Q31.2) MUTATED    54   3   5   6
  AMP PEAK 19(7Q31.2) WILD-TYPE 297  19  12  24
D19V5, multiclass
    clus
vv   AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE
  R0                          54                           297
  R1                           3                            19
  R2                           5                            12
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(7Q31.2) MUTATED                                  0     3
  AMP PEAK 19(7Q31.2) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(7Q31.2) MUTATED                          14
  AMP PEAK 19(7Q31.2) WILD-TYPE                        76
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(7Q31.2) MUTATED                                           0    62
  AMP PEAK 19(7Q31.2) WILD-TYPE                                         9   295
D19V6, multiclass
                                           clus
vv                                          AMP PEAK 19(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              62
                                           clus
vv                                          AMP PEAK 19(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               295
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(7Q31.2) MUTATED     1  63
  AMP PEAK 19(7Q31.2) WILD-TYPE  12 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(7Q31.2) MUTATED      1   63
  AMP PEAK 19(7Q31.2) WILD-TYPE   12  287
                        clus
vv                       AMP PEAK 19(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       AMP PEAK 19(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           287
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(8P11.22) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(8P11.22) MUTATED    99  20
  AMP PEAK 20(8P11.22) WILD-TYPE 344  40
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                           119                            384 
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                            20                             40 
$`AMP PEAK 20(8P11.22) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ 
       37.02       105.37        23.21        17.59        11.44         9.60 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       28.64         7.33        14.96         0.39        19.79         2.40 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NE 
        0.49         2.24         1.68         1.64         1.28        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A0L8 
       15.62         0.76         1.87         0.13        39.42        48.79 
TCGA-AP-A0LD TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A5FX TCGA-AX-A0IW 
      117.99        33.40        31.30        30.90        33.73        37.78 
TCGA-AX-A1CA TCGA-AX-A1CI TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       20.28        72.56         4.77        71.24        33.53        68.71 
TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-B5-A0JT TCGA-B5-A0K4 
       33.40         0.10         0.20        20.52        43.13        17.88 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
        4.11         8.71        32.09        33.50        27.35        19.56 
TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-BG-A0M0 TCGA-BG-A0M2 
      102.31        14.70       116.25        33.11        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MQ TCGA-BG-A0YU TCGA-BG-A18C 
       34.98        28.27        10.72        39.32        14.83        15.45 
TCGA-BG-A221 TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC 
        1.81        23.70         6.81        35.90         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG 
       10.16        24.13        16.64        46.95         4.80        77.95 
TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZU TCGA-D1-A102 
       67.20        73.25        49.55        63.16        28.67         4.44 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A17K 
        0.66        36.10        37.32        31.07         0.69        28.08 
TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       11.15        13.22         2.07         3.52        41.42         8.48 
TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 
       24.30        31.10        48.36        17.06        24.33        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EY-A1G8 
       18.81        33.01        57.60        24.79        19.40        14.99 
TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GV 
        4.54         6.90        19.27        17.88        17.62        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
        6.48        19.33        14.40        22.82        13.45        29.10 
TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-K6-A3WQ 
       17.92         6.97         7.99        26.01        13.15 

$`AMP PEAK 20(8P11.22) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95         7.92        36.33         8.02        91.04        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM 
        5.33         5.16         1.18         1.08         1.97         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        3.02         1.12         0.76        14.66        22.49        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3QS 
        0.92        36.99         1.35         1.94        15.95        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 
        1.71         2.33         0.99         2.70        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H 
        5.95        23.31        86.07         8.22        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       125.42       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
        3.39        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ 
       25.08        71.67        60.36        55.89        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
       49.15         6.71        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        12.43        20.05        76.83 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39        11.08        30.12 
TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       61.18        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX 
        2.96        31.13        38.70         0.23         0.33         0.13 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        80.38        56.91        46.75        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F 
       23.01        13.74        17.10        17.85        11.01       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       40.50        36.82        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-A1MY 
       16.57       191.84        50.89        14.40        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 
       15.29        12.79        96.30        78.81        62.14         5.03 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
        7.92        38.37        36.49        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA 
       14.27         9.57        35.67        20.12        11.31        34.98 
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        23.47 
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        88.34        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-A0ZO 
       59.51        62.79        63.58        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       29.95         8.55         0.56         4.87        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-A167 TCGA-D1-A16B TCGA-D1-A16D 
        3.68        29.33        32.58        15.72        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-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         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         6.77         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-A1NW 
        1.78        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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        35.38         9.37        12.39        91.96 
TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       23.38         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A2CG TCGA-EO-A3AS 
       37.71        31.96        35.05        27.12        32.38        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       16.34         6.21         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GS 
       23.34        23.90        22.78        13.97        18.84        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
       16.11        12.43         8.55        12.59         3.62        18.87 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        27.35        13.84         6.44         2.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        3.72         5.29         5.88        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       36.00        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        41.06        45.01         1.74 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
        2.43        10.82         9.11        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                        117.99                         191.84 
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                        19.330                         23.685 
[1] "0.1 - 118.0 (19.3)" "0.0 - 191.8 (23.7)"
[1] "hr=" "1.9"
D20V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 20(8P11.22) MUTATED                                        90
  AMP PEAK 20(8P11.22) WILD-TYPE                                     290
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 20(8P11.22) MUTATED                               6
  AMP PEAK 20(8P11.22) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 20(8P11.22) MUTATED                                  24
  AMP PEAK 20(8P11.22) WILD-TYPE                                80
D20V3, multiclass
                                         clus
vv                                        AMP PEAK 20(8P11.22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           90
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 24
                                         clus
vv                                        AMP PEAK 20(8P11.22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            290
  MIXED SEROUS AND ENDOMETRIOID                                       15
  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"
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(8P11.22) MUTATED    28  92
  AMP PEAK 20(8P11.22) WILD-TYPE 110 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(8P11.22) MUTATED     28   92
  AMP PEAK 20(8P11.22) WILD-TYPE  110  275
     clus
vv    AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE
  NO                            28                            110
  YES                           92                            275
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(8P11.22) MUTATED    83   4   5   9
  AMP PEAK 20(8P11.22) WILD-TYPE 268  18  12  21
D20V5, multiclass
    clus
vv   AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE
  R0                           83                            268
  R1                            4                             18
  R2                            5                             12
  RX                            9                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(8P11.22) MUTATED                                  0     6
  AMP PEAK 20(8P11.22) WILD-TYPE                                4    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(8P11.22) MUTATED                          23
  AMP PEAK 20(8P11.22) WILD-TYPE                        67
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 20(8P11.22) MUTATED                                           4
  AMP PEAK 20(8P11.22) WILD-TYPE                                         5
                                vv
clus                             WHITE
  AMP PEAK 20(8P11.22) MUTATED      81
  AMP PEAK 20(8P11.22) WILD-TYPE   276
D20V6, multiclass
                                           clus
vv                                          AMP PEAK 20(8P11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            4
  WHITE                                                               81
                                           clus
vv                                          AMP PEAK 20(8P11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              5
  WHITE                                                                276
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(8P11.22) MUTATED     2  90
  AMP PEAK 20(8P11.22) WILD-TYPE  11 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(8P11.22) MUTATED      2   90
  AMP PEAK 20(8P11.22) WILD-TYPE   11  260
                        clus
vv                       AMP PEAK 20(8P11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       AMP PEAK 20(8P11.22) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            260
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(8P11.21) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(8P11.21) MUTATED   122  30
  AMP PEAK 21(8P11.21) WILD-TYPE 321  30
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                           152                            351 
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                            30                             30 
$`AMP PEAK 21(8P11.21) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OJ 
       37.02       105.37        23.21        17.59        11.44         9.60 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL 
       28.64         7.33        14.96         1.08         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3IA 
        2.40         0.49         2.24         1.68         1.64         0.92 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW 
       20.65        15.62         0.76         1.87        16.87         0.13 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF 
       21.99        45.53        48.79       125.42       117.99         3.39 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW 
       33.40        31.30        30.90        18.25        33.73        37.78 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 
       20.28        12.43        72.56         4.77        30.12        33.53 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 
       68.71        33.40        38.70         0.10         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A0K8 
        0.03         0.13        80.38        43.13        17.88        17.85 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
        4.11         8.71        32.09        33.50        27.35        19.56 
TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE 
      102.31        14.70        11.87       116.25        33.11        34.95 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       19.33        20.94        34.98        36.49        28.27        10.72 
TCGA-BG-A0MQ TCGA-BG-A0YU TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE TCGA-BG-A3PP 
       39.32        14.83        15.45         1.81        23.70         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0T9 
       35.90         6.21        10.22        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        67.20        73.25        49.55        63.16 
TCGA-D1-A0ZU TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 
       28.67         4.44        39.48         0.66        36.10        37.32 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17R TCGA-D1-A1NU 
       11.51        31.07         0.69        18.67        11.15        13.22 
TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A1C3 
        2.07         3.52        41.42         8.48         4.11        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        91.96        48.36 
TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22T 
       17.06        24.33        10.92        18.81        37.71        33.01 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EY-A1G8 TCGA-EY-A1GC 
       24.79        32.38        19.40        26.96        14.99         4.54 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV 
        6.90        19.27        17.88        17.62        15.09        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33         3.62        14.40        22.82        13.45 
TCGA-EY-A2OQ TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2EU 
       29.10         6.97         5.88        36.00         7.99        96.69 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-PG-A7D5 
        9.07        28.93        26.01        41.06        13.15        23.97 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`AMP PEAK 21(8P11.21) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95         7.92        36.33         8.02        91.04        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO 
        5.33         5.16         1.18         1.97         0.85         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.12         0.76        14.66        22.49        22.26         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DW 
       36.99         1.35         1.94        15.95         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.99         2.70        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
       20.91       110.37        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        55.89        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       41.95        49.15         6.71        10.42        27.85        16.24 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ 
       16.96        13.55        15.25        20.05        76.83        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 
       67.50        25.12        36.39        11.08        71.24        61.18 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 
       31.13         0.23         0.33         0.13         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18         8.35        14.47        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F 
       25.91        23.01        13.74        17.10        11.01       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       40.50        36.82        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       191.84        50.89        14.40        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       12.79        96.30        78.81        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 
       34.13        18.61        20.19        35.21         7.92        38.37 
TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MS 
       41.52        48.56        23.47        43.30        43.04        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 
       34.29        52.64        52.83        56.58        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        14.27         9.57        35.67 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       20.12        11.31        34.98        10.16        31.76        24.99 
TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       13.18        10.03         9.86        23.47        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        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.58        66.48        16.83        19.79        29.95         8.55 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 
        0.56         4.87        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-A167 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       15.72        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         1.41         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         6.77         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-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-DF-A2KZ 
        1.05         3.95        44.88         0.26         4.27        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 
       16.31        39.29        36.62        23.38         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U 
       16.01         7.36        16.80        31.96        35.05        27.12 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       57.60        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       22.26        16.34         6.21         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       23.34        23.34        23.90        22.78        13.97        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OO 
       16.11        12.43         8.55        12.59        18.87        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        27.35        13.84         6.44        17.92         2.14 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D5 
        3.72         5.29        40.01        34.98        33.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR 
        8.98        59.01        28.96        25.02        45.01         1.74 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        2.43        10.82         9.11        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                          0.03                           0.13 
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                        125.42                         191.84 
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                          19.3                           24.3 
[1] "0.0 - 125.4 (19.3)" "0.1 - 191.8 (24.3)"
[1] "hr=" "2.7"
D21V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 21(8P11.21) MUTATED                                        90
  AMP PEAK 21(8P11.21) WILD-TYPE                                     290
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 21(8P11.21) MUTATED                               7
  AMP PEAK 21(8P11.21) WILD-TYPE                            14
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 21(8P11.21) MUTATED                                  56
  AMP PEAK 21(8P11.21) WILD-TYPE                                48
D21V3, multiclass
                                         clus
vv                                        AMP PEAK 21(8P11.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           90
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 56
                                         clus
vv                                        AMP PEAK 21(8P11.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            290
  MIXED SEROUS AND ENDOMETRIOID                                       14
  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"
D21V4, binary
                                cls
clus                               0   1
  AMP PEAK 21(8P11.21) MUTATED    31 122
  AMP PEAK 21(8P11.21) WILD-TYPE 107 245
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(8P11.21) MUTATED     31  122
  AMP PEAK 21(8P11.21) WILD-TYPE  107  245
     clus
vv    AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE
  NO                            31                            107
  YES                          122                            245
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(8P11.21) MUTATED   101   4  11  12
  AMP PEAK 21(8P11.21) WILD-TYPE 250  18   6  18
D21V5, multiclass
    clus
vv   AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE
  R0                          101                            250
  R1                            4                             18
  R2                           11                              6
  RX                           12                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(8P11.21) MUTATED                                  1     7
  AMP PEAK 21(8P11.21) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(8P11.21) MUTATED                          34
  AMP PEAK 21(8P11.21) WILD-TYPE                        56
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 21(8P11.21) MUTATED                                           4
  AMP PEAK 21(8P11.21) WILD-TYPE                                         5
                                vv
clus                             WHITE
  AMP PEAK 21(8P11.21) MUTATED      99
  AMP PEAK 21(8P11.21) WILD-TYPE   258
D21V6, multiclass
                                           clus
vv                                          AMP PEAK 21(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            4
  WHITE                                                               99
                                           clus
vv                                          AMP PEAK 21(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             56
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              5
  WHITE                                                                258
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(8P11.21) MUTATED     3 112
  AMP PEAK 21(8P11.21) WILD-TYPE  10 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(8P11.21) MUTATED      3  112
  AMP PEAK 21(8P11.21) WILD-TYPE   10  238
                        clus
vv                       AMP PEAK 21(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       AMP PEAK 21(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            238
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(8Q24.21) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(8Q24.21) MUTATED   159  34
  AMP PEAK 22(8Q24.21) WILD-TYPE 284  26
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                           193                            310 
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                            34                             26 
$`AMP PEAK 22(8Q24.21) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0R7 
       37.02       105.37        65.75        36.82        23.21        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO 
       11.44        36.33         9.60        91.04        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD 
       14.96         1.18         0.39        19.79         2.40         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.12         2.24         1.68         1.64        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL 
        0.92        20.65         1.35        15.62         0.76         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A05H 
       16.87         1.71         0.99         0.13        39.42        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        41.95        30.90        18.25         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI 
       16.96        13.55        20.28        12.43        76.83        72.56 
TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       67.50        11.08         4.77        30.12        71.24        33.53 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW 
       68.71        33.40         2.96        38.70         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.13         0.20        20.52         0.03         0.23         0.13 
TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11H 
       80.38        43.13        17.88         4.11         8.71        88.34 
TCGA-B5-A11I TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR 
       75.72        32.09        33.50        27.35        19.56       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FB 
      102.31        50.89        14.70        12.79       116.25        78.81 
TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 
       33.11        34.13        34.95        19.33        20.94        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MT TCGA-BG-A0YU 
        7.92        36.49        28.27        10.72        21.17        14.83 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB 
       15.45         1.81        23.70         6.81        35.90         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A6W4 TCGA-BS-A0T9 
       10.22        10.16        24.13        16.64         9.86        46.95 
TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP 
        4.80        77.95        67.20        73.25        63.16        29.95 
TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 
       28.67        22.55         4.44        39.48         0.66        36.10 
TCGA-D1-A169 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S 
       37.32        27.42        11.51        31.07         0.69        18.67 
TCGA-D1-A179 TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 
        6.77        11.15        13.22         0.72         2.07         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1C3 TCGA-DI-A1NN 
       41.42         8.48        44.88         4.11        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 
        9.37        12.39        91.96        48.36        17.06        24.33 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG 
       10.92        18.81        37.71        33.01        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G8 
       19.40        34.39        27.16        26.96        22.26        14.99 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR 
        4.54        23.90         6.90        19.27        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A2OM 
       15.09        15.81         6.48        19.33        14.40        22.82 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
        6.97         5.88         7.99        96.69         9.07        28.93 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       26.01        41.06         1.74        13.15        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 22(8Q24.21) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
        3.22        87.32        74.10        57.53        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        28.27        20.81        68.65        19.96 
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         7.92 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O 
        8.02        46.32         5.33         5.16         1.08         1.97 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        0.85         3.02         0.76        14.66        22.49        36.99 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 
        1.94        15.95         2.33         2.70        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
        7.86        12.20        20.91       110.37         3.39        63.16 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       35.54        49.15         6.71        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H8 
       15.25        20.05        54.12        25.12        36.39        61.18 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A3FS TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.23         0.13         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        23.01        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L 
       17.85        11.01       185.79       113.36        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y 
       43.96        40.50        36.82        16.73        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       17.36        16.57        14.40        11.70        11.87        15.29 
TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       96.30        62.14         5.03        41.06        18.61        20.19 
TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       35.21        38.37        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       43.04        39.32        30.81        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B 
        9.57        35.67        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        23.47        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        88.34 
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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       63.58        49.55        66.48        16.83        19.79         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-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-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       36.36        37.51        36.79        29.92        33.63        10.65 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         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-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG 
       18.02        15.06         1.05         3.95         0.26         4.27 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A2QU TCGA-E6-A1LX 
       27.16        16.31        39.29        36.62        31.10        23.38 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R 
        2.37         6.67        16.01         7.36        16.80        31.96 
TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       35.05        27.12        57.60        19.36        35.15        12.89 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       16.34         6.21         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       23.34        22.78        13.97        18.84        16.11        12.43 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP 
        8.55        12.59         3.62        18.87        45.76        31.04 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 
       36.00        13.84         8.98        59.01        28.96        25.02 
TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       45.01         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                          0.03                           0.13 
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                        191.84                         185.79 
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                        19.330                         24.505 
[1] "0.0 - 191.8 (19.3)" "0.1 - 185.8 (24.5)"
[1] "hr=" "2.4"
D22V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 22(8Q24.21) MUTATED                                       109
  AMP PEAK 22(8Q24.21) WILD-TYPE                                     271
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 22(8Q24.21) MUTATED                              10
  AMP PEAK 22(8Q24.21) WILD-TYPE                            11
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 22(8Q24.21) MUTATED                                  75
  AMP PEAK 22(8Q24.21) WILD-TYPE                                29
D22V3, multiclass
                                         clus
vv                                        AMP PEAK 22(8Q24.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          109
  MIXED SEROUS AND ENDOMETRIOID                                     10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 75
                                         clus
vv                                        AMP PEAK 22(8Q24.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            271
  MIXED SEROUS AND ENDOMETRIOID                                       11
  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"
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(8Q24.21) MUTATED    40 154
  AMP PEAK 22(8Q24.21) WILD-TYPE  98 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(8Q24.21) MUTATED     40  154
  AMP PEAK 22(8Q24.21) WILD-TYPE   98  213
     clus
vv    AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE
  NO                            40                             98
  YES                          154                            213
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(8Q24.21) MUTATED   131   6  10  13
  AMP PEAK 22(8Q24.21) WILD-TYPE 220  16   7  17
D22V5, multiclass
    clus
vv   AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE
  R0                          131                            220
  R1                            6                             16
  R2                           10                              7
  RX                           13                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(8Q24.21) MUTATED                                  1     7
  AMP PEAK 22(8Q24.21) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(8Q24.21) MUTATED                          45
  AMP PEAK 22(8Q24.21) WILD-TYPE                        45
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 22(8Q24.21) MUTATED                                           3
  AMP PEAK 22(8Q24.21) WILD-TYPE                                         6
                                vv
clus                             WHITE
  AMP PEAK 22(8Q24.21) MUTATED     127
  AMP PEAK 22(8Q24.21) WILD-TYPE   230
D22V6, multiclass
                                           clus
vv                                          AMP PEAK 22(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           45
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                              127
                                           clus
vv                                          AMP PEAK 22(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             45
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                230
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(8Q24.21) MUTATED     4 140
  AMP PEAK 22(8Q24.21) WILD-TYPE   9 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(8Q24.21) MUTATED      4  140
  AMP PEAK 22(8Q24.21) WILD-TYPE    9  210
                        clus
vv                       AMP PEAK 22(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          140
                        clus
vv                       AMP PEAK 22(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            210
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(8Q24.21) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(8Q24.21) MUTATED   165  34
  AMP PEAK 23(8Q24.21) WILD-TYPE 278  26
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                           199                            304 
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                            34                             26 
$`AMP PEAK 23(8Q24.21) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG 
       37.02       105.37        65.75        23.21        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       36.33         9.60        91.04        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF 
        1.18         0.39        19.79         2.40         0.49         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        2.24         1.68         1.64        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL 
       36.99        20.65         1.35        15.62         0.76         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05H 
       16.87         1.71         0.13        21.99        39.42        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO 
       48.79       125.42       117.99         3.39        97.71        33.40 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E0 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW 
       31.30        41.95        30.90        18.25         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       16.96        13.55        15.25        20.28        12.43        76.83 
TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       72.56        67.50        11.08         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FT 
       33.53        68.71        33.40         2.96        38.70         0.10 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.13         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A11E TCGA-B5-A11H 
        0.13        80.38        43.13        17.88         8.71        88.34 
TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11V 
       75.72        45.90        32.09        33.50        27.35        19.56 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1N2 TCGA-B5-A3F9 
      191.84       102.31        50.89        14.70        12.79       116.25 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 
       33.11         5.03        34.13        34.95        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG 
       34.98         7.92        36.49        28.27        10.72        48.56 
TCGA-BG-A0MT TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE 
       21.17        12.56        14.73        15.45         1.81        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
        6.81        35.90         6.21        10.22        10.16        24.13 
TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 
       16.64        46.95        23.47         4.80        77.95        67.20 
TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A102 
       73.25        63.16        29.95        28.67        22.55         4.44 
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         6.77        11.15        22.92 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       13.22         0.72         2.07         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       44.88         4.11        24.30        35.38         9.37        12.39 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       91.96        48.36        17.06        24.33        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       37.71        33.01        24.79        32.38        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GJ 
       27.16        26.96        22.26        14.99         4.54        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV 
        6.90        19.27        17.88        17.62        15.09        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
        6.97         5.88         7.99        96.69         9.07        28.93 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       26.01        41.06         1.74        13.15        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 23(8Q24.21) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
        3.22        87.32        74.10        57.53        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GX 
       46.55        38.37        36.82        28.27        20.81        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N 
        7.92         8.02        46.32         5.33         5.16         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.97         0.85         3.02         0.76        14.66        22.49 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
        1.94        15.95         2.33         0.99         2.70        83.67 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
        7.86        12.20        20.91       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       35.54        49.15         6.71        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H8 TCGA-AX-A2HD 
       20.05        54.12        25.12        36.39        61.18        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       19.36        26.33        17.75        27.32        31.13         0.23 
TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.33         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        23.01        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11N 
       11.01         4.11       185.79       113.36        54.44        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       40.50        36.82        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        14.40        11.70        11.87        15.29        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 
       78.81        62.14        41.06        18.61        20.19        35.21 
TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       38.37        41.52        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       30.81        20.28        15.42        24.39        26.66        16.34 
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-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       14.01        15.45        14.27         9.57        35.67        20.12 
TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       11.31        34.98        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
        9.86        85.55        78.21        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        88.34        85.84        82.39        81.57 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       72.72        59.51        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV 
       16.83        19.79         8.55         0.56         4.87        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-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         1.41         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-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-A17S TCGA-D1-A17T TCGA-D1-A1NS 
       10.22         1.51         1.78        24.30         2.33         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-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       31.10        23.38         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU 
       16.80        31.96        35.05        27.12        57.60        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE 
       35.15        12.89        16.34         6.21         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       27.16        23.34        23.34        22.78        13.97        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A2OP 
       16.11        12.43         8.55        12.59        45.76        31.04 
TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 
       36.00        13.84         8.98        59.01        28.96        25.02 
TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       45.01         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                          0.03                           0.23 
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                        191.84                         185.79 
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                         19.33                          25.05 
[1] "0.0 - 191.8 (19.3)" "0.2 - 185.8 (25.0)"
[1] "hr=" "2.3"
D23V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 23(8Q24.21) MUTATED                                       112
  AMP PEAK 23(8Q24.21) WILD-TYPE                                     268
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 23(8Q24.21) MUTATED                               9
  AMP PEAK 23(8Q24.21) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 23(8Q24.21) MUTATED                                  79
  AMP PEAK 23(8Q24.21) WILD-TYPE                                25
D23V3, multiclass
                                         clus
vv                                        AMP PEAK 23(8Q24.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          112
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 79
                                         clus
vv                                        AMP PEAK 23(8Q24.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            268
  MIXED SEROUS AND ENDOMETRIOID                                       12
  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"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(8Q24.21) MUTATED    41 159
  AMP PEAK 23(8Q24.21) WILD-TYPE  97 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(8Q24.21) MUTATED     41  159
  AMP PEAK 23(8Q24.21) WILD-TYPE   97  208
     clus
vv    AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE
  NO                            41                             97
  YES                          159                            208
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(8Q24.21) MUTATED   135   6  13  12
  AMP PEAK 23(8Q24.21) WILD-TYPE 216  16   4  18
D23V5, multiclass
    clus
vv   AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE
  R0                          135                            216
  R1                            6                             16
  R2                           13                              4
  RX                           12                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(8Q24.21) MUTATED                                  1     7
  AMP PEAK 23(8Q24.21) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(8Q24.21) MUTATED                          41
  AMP PEAK 23(8Q24.21) WILD-TYPE                        49
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 23(8Q24.21) MUTATED                                           5
  AMP PEAK 23(8Q24.21) WILD-TYPE                                         4
                                vv
clus                             WHITE
  AMP PEAK 23(8Q24.21) MUTATED     135
  AMP PEAK 23(8Q24.21) WILD-TYPE   222
D23V6, multiclass
                                           clus
vv                                          AMP PEAK 23(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           41
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            5
  WHITE                                                              135
                                           clus
vv                                          AMP PEAK 23(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             49
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              4
  WHITE                                                                222
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(8Q24.21) MUTATED     5 143
  AMP PEAK 23(8Q24.21) WILD-TYPE   8 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(8Q24.21) MUTATED      5  143
  AMP PEAK 23(8Q24.21) WILD-TYPE    8  207
                        clus
vv                       AMP PEAK 23(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       AMP PEAK 23(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            207
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(9P24.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 24(9P24.2) MUTATED    48  13
  AMP PEAK 24(9P24.2) WILD-TYPE 395  47
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           61                           442 
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           13                            47 
$`AMP PEAK 24(9P24.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QM 
       37.02        11.44        91.04        14.96         0.39         0.85 
TCGA-AJ-A3EM TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A5FX TCGA-AX-A05Z TCGA-AX-A06B 
       22.26        36.89       125.42        33.73        46.45        53.92 
TCGA-AX-A06F TCGA-AX-A0IU TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF 
       51.09        28.54        11.08        30.12        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
        2.96        20.52         0.03         0.13        80.38        23.01 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-BG-A0M6 TCGA-BG-A0YV 
       88.34        75.72        11.87         5.03         7.92        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16N 
        6.81        10.22        24.13        61.87        67.20        31.07 
TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-DI-A2QU TCGA-E6-A1M0 TCGA-E6-A8L9 
        6.77         0.72        44.88        31.10        17.06        24.33 
TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GS 
       37.71        57.60        16.34         4.54        17.62        15.09 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR 
        8.55         3.62        13.45        29.10        13.84         6.44 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A7D5 
       96.69        26.01        41.06        45.01         1.74        23.97 
TCGA-PG-A914 
       12.92 

$`AMP PEAK 24(9P24.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
        7.33         1.18         1.08         1.97        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        3.02         0.49         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.64        14.66        22.49         1.28         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.87        16.87         1.71         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        45.53         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       18.25         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       72.03        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       33.53        68.71        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.13         0.20         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
        8.71       185.79       113.36        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
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-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        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         6.21        10.16        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 
       23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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 
        1.41         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42         8.48         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        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        91.96        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y 
       18.81        31.96        35.05        33.01        27.12        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       27.16        26.96        22.26         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT 
       13.97         6.90        19.27        18.84        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A547 
       18.87        22.82        45.76        31.04        27.35        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
        2.14         6.97         3.72         5.29         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-K6-A3WQ 
       59.01         9.07        28.93        28.96        25.02        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
        2.43        10.82         9.11         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                        22.26                         22.87 
[1] "0.0 - 125.4 (22.3)" "0.1 - 191.8 (22.9)"
[1] "hr=" "2"  
D24V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 24(9P24.2) MUTATED                                        23
  AMP PEAK 24(9P24.2) WILD-TYPE                                     357
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 24(9P24.2) MUTATED                               3
  AMP PEAK 24(9P24.2) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 24(9P24.2) MUTATED                                  35
  AMP PEAK 24(9P24.2) WILD-TYPE                                69
D24V3, multiclass
                                         clus
vv                                        AMP PEAK 24(9P24.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          23
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                35
                                         clus
vv                                        AMP PEAK 24(9P24.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           357
  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"
D24V4, binary
                               cls
clus                              0   1
  AMP PEAK 24(9P24.2) MUTATED    12  49
  AMP PEAK 24(9P24.2) WILD-TYPE 126 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(9P24.2) MUTATED     12   49
  AMP PEAK 24(9P24.2) WILD-TYPE  126  318
     clus
vv    AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE
  NO                           12                           126
  YES                          49                           318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 24(9P24.2) MUTATED    39   3   3   6
  AMP PEAK 24(9P24.2) WILD-TYPE 312  19  14  24
D24V5, multiclass
    clus
vv   AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE
  R0                          39                           312
  R1                           3                            19
  R2                           3                            14
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(9P24.2) MUTATED                                  0     1
  AMP PEAK 24(9P24.2) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(9P24.2) MUTATED                          18
  AMP PEAK 24(9P24.2) WILD-TYPE                        72
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 24(9P24.2) MUTATED                                           1    36
  AMP PEAK 24(9P24.2) WILD-TYPE                                         8   321
D24V6, multiclass
                                           clus
vv                                          AMP PEAK 24(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              36
                                           clus
vv                                          AMP PEAK 24(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                              0   1
  AMP PEAK 24(9P24.2) MUTATED     5  40
  AMP PEAK 24(9P24.2) WILD-TYPE   8 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(9P24.2) MUTATED      5   40
  AMP PEAK 24(9P24.2) WILD-TYPE    8  310
                        clus
vv                       AMP PEAK 24(9P24.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          40
                        clus
vv                       AMP PEAK 24(9P24.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           310
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(9Q34.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 25(9Q34.3) MUTATED    29   8
  AMP PEAK 25(9Q34.3) WILD-TYPE 414  52
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                           37                           466 
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                            8                            52 
$`AMP PEAK 25(9Q34.3) MUTATED`
TCGA-A5-A0GN TCGA-A5-A0GU TCGA-A5-A1OH TCGA-AJ-A2QM TCGA-AJ-A3EJ TCGA-AP-A052 
       60.53        28.27        36.33         0.85         1.64        21.99 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0LH TCGA-AW-A1PO TCGA-AX-A0IU 
       39.42        57.80        36.89        36.36         0.56        28.54 
TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-B5-A0K3 
       71.24         2.96        38.70         0.03         0.23        23.01 
TCGA-B5-A0KB TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-BK-A139 TCGA-D1-A16I TCGA-D1-A1NX 
        4.11        12.79        34.13        10.16        11.51        18.25 
TCGA-E6-A1M0 TCGA-EO-A2CG TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A212 
       17.06        32.38        23.90        15.09        12.59         3.62 
TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A7D5 TCGA-PG-A914 
       17.92        34.98        26.01         1.74        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 25(9Q34.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GV 
       65.75        60.53        46.55        38.37        36.82        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        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         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        2.24         1.68        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        0.99         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        45.53         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       16.96        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08         4.77        30.12        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
       20.52         0.13         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E 
       17.88        13.74        17.10        17.85        11.01         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11         5.03        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        10.22        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        23.47 
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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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         1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        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-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        91.96        23.38        48.36         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       24.33        16.01         7.36        16.80        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       31.04        29.10        27.35        13.84         6.44         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
        6.97         3.72         5.29         5.88        40.01        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       36.00         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.07        28.93        28.96        25.02        41.06        45.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.15         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                        71.24                        191.84 
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                       18.250                        23.065 
[1] "0.0 - 71.2 (18.2)"  "0.1 - 191.8 (23.1)"
[1] "hr=" "2.5"
D25V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 25(9Q34.3) MUTATED                                        12
  AMP PEAK 25(9Q34.3) WILD-TYPE                                     368
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 25(9Q34.3) MUTATED                               4
  AMP PEAK 25(9Q34.3) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 25(9Q34.3) MUTATED                                  21
  AMP PEAK 25(9Q34.3) WILD-TYPE                                83
D25V3, multiclass
                                         clus
vv                                        AMP PEAK 25(9Q34.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          12
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                21
                                         clus
vv                                        AMP PEAK 25(9Q34.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           368
  MIXED SEROUS AND ENDOMETRIOID                                      17
  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"
D25V4, binary
                               cls
clus                              0   1
  AMP PEAK 25(9Q34.3) MUTATED    10  27
  AMP PEAK 25(9Q34.3) WILD-TYPE 128 340
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(9Q34.3) MUTATED     10   27
  AMP PEAK 25(9Q34.3) WILD-TYPE  128  340
     clus
vv    AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE
  NO                           10                           128
  YES                          27                           340
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 25(9Q34.3) MUTATED    26   2   2   0
  AMP PEAK 25(9Q34.3) WILD-TYPE 325  20  15  30
D25V5, multiclass
    clus
vv   AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE
  R0                          26                           325
  R1                           2                            20
  R2                           2                            15
  RX                           0                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(9Q34.3) MUTATED                                  0     1
  AMP PEAK 25(9Q34.3) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(9Q34.3) MUTATED                          16
  AMP PEAK 25(9Q34.3) WILD-TYPE                        74
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 25(9Q34.3) MUTATED                                           0    20
  AMP PEAK 25(9Q34.3) WILD-TYPE                                         9   337
D25V6, multiclass
                                           clus
vv                                          AMP PEAK 25(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              20
                                           clus
vv                                          AMP PEAK 25(9Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            74
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               337
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                               cls
clus                              0   1
  AMP PEAK 25(9Q34.3) MUTATED     0  24
  AMP PEAK 25(9Q34.3) WILD-TYPE  13 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(9Q34.3) MUTATED      0   24
  AMP PEAK 25(9Q34.3) WILD-TYPE   13  326
                        clus
vv                       AMP PEAK 25(9Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          24
                        clus
vv                       AMP PEAK 25(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           326
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(10Q22.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(10Q22.2) MUTATED   117  19
  AMP PEAK 26(10Q22.2) WILD-TYPE 326  41
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                           136                            367 
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                            19                             41 
$`AMP PEAK 26(10Q22.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0R9 
       37.02       105.37        65.75        28.27        20.81        24.62 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QM 
       36.33         9.60        91.04         1.18         1.97         0.85 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NH TCGA-AJ-A3QS 
        2.24         1.64         1.28        36.99         0.76        16.87 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
        5.95        39.42        36.89        20.91        48.79       117.99 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ TCGA-AP-A1E3 TCGA-AP-A1E4 
       97.71        31.73        82.52        80.78        27.85        16.24 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A06J 
       13.58        19.82        29.69        68.35        12.26        30.02 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CJ 
       28.54        37.78        13.28        20.28        12.43        54.12 
TCGA-AX-A2H2 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-B5-A0JT 
        4.77        17.75         2.96         0.33         0.13        43.13 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11Q 
       17.85         8.71       185.79        75.72        45.90        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MV TCGA-B5-A5OD TCGA-BG-A0LX TCGA-BG-A0M2 
       33.50        27.35        14.40        34.13        20.19        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0MG TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT 
       35.21         7.92        48.56        30.81        15.42        24.39 
TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CC 
       56.58        14.73        14.01         6.81        35.90        10.22 
TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0UV TCGA-BS-A0V7 
       16.64        46.95        61.87        30.74        73.25        63.58 
TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZU TCGA-D1-A102 
       49.55        66.48        29.95         8.55        28.67         4.44 
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-A2G5 
        0.69        18.67         2.33        18.25         2.07        41.42 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1M0 TCGA-E6-A2P9 
        4.11        35.38         9.37        12.39        17.06         6.67 
TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU 
       18.81        24.79        32.38        19.40        26.96        22.26 
TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS 
        6.21         4.54        23.34        19.27        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       16.11         8.55         6.48        19.33        12.59        14.40 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A72D TCGA-FI-A2D4 
       45.76        31.04        29.10        27.35         5.88         7.99 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PX 
       96.69        59.01         9.07        28.93        25.02        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A915 
        1.74        13.15        23.97         7.00 

$`AMP PEAK 26(10Q22.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
        3.22        87.32        74.10        57.53        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       46.55        38.37        36.82        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       17.59        19.59        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
       11.44         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        7.33        14.96         1.08         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        3.02         0.49         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        22.26         0.92        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L9 
        8.22        57.80        45.53         7.86        12.20       125.42 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37         3.39        63.16        36.36        83.97        27.12 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       33.40        61.64        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
        6.71        30.90        10.42        18.25        33.73         0.56 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       53.92        51.09        27.39        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        19.20        16.96        13.55        15.25 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        76.83        72.56        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       11.08        30.12        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN 
       33.40        40.50        19.36        26.33        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       38.70         0.23         0.10         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       80.38        56.91        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11G 
       17.88        13.74        17.10        11.01         4.11       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U 
       88.34        54.44        43.96        40.50        36.82        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        50.89        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M4 
        5.03        41.06        34.95        18.61        19.33        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI 
       38.37        36.49        28.27        10.72        41.52        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV 
       43.30        43.04        39.32        21.17        20.28        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        52.64        52.83        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       13.78        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB 
       35.67        23.70        20.12        11.31        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        31.76        24.99        24.13        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TE TCGA-BS-A0TG 
        9.86        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF 
       67.99        96.49        97.41        67.20        88.34        85.84 
TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0VI 
       82.39        81.57        72.72        59.51        62.79        63.16 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       16.83        19.79         0.56         4.87        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A160 TCGA-D1-A163 
        1.74        21.99        30.08        29.88         3.68        32.58 
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-A16V TCGA-D1-A16X 
       11.51        29.92        33.63        10.65         1.41         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         6.77 
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-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY 
       24.30        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         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30        31.10        91.96        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW 
       34.39        19.36        35.15        12.89        27.16        16.34 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
       14.99         8.15        24.36        27.16        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GU 
       22.78        13.97         6.90        18.84        17.62        12.43 
TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A3QX 
       15.81         3.62        18.87        22.82        13.45        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99        36.00        13.84         8.98 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       28.96        26.01        41.06         2.43        10.82         9.11 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       12.92        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                        185.79                         191.84 
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                        20.925                         23.010 
[1] "0.1 - 185.8 (20.9)" "0.0 - 191.8 (23.0)"
[1] "hr=" "1.3"
D26V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 26(10Q22.2) MUTATED                                        91
  AMP PEAK 26(10Q22.2) WILD-TYPE                                     289
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 26(10Q22.2) MUTATED                               3
  AMP PEAK 26(10Q22.2) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 26(10Q22.2) MUTATED                                  42
  AMP PEAK 26(10Q22.2) WILD-TYPE                                62
D26V3, multiclass
                                         clus
vv                                        AMP PEAK 26(10Q22.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           91
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 42
                                         clus
vv                                        AMP PEAK 26(10Q22.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            289
  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"
D26V4, binary
                                cls
clus                               0   1
  AMP PEAK 26(10Q22.2) MUTATED    34 102
  AMP PEAK 26(10Q22.2) WILD-TYPE 104 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(10Q22.2) MUTATED     34  102
  AMP PEAK 26(10Q22.2) WILD-TYPE  104  265
     clus
vv    AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE
  NO                            34                            104
  YES                          102                            265
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(10Q22.2) MUTATED    99   7   7   7
  AMP PEAK 26(10Q22.2) WILD-TYPE 252  15  10  23
D26V5, multiclass
    clus
vv   AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE
  R0                           99                            252
  R1                            7                             15
  R2                            7                             10
  RX                            7                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(10Q22.2) MUTATED                                  2     5
  AMP PEAK 26(10Q22.2) WILD-TYPE                                2    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(10Q22.2) MUTATED                          24
  AMP PEAK 26(10Q22.2) WILD-TYPE                        66
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 26(10Q22.2) MUTATED                                           4
  AMP PEAK 26(10Q22.2) WILD-TYPE                                         5
                                vv
clus                             WHITE
  AMP PEAK 26(10Q22.2) MUTATED      95
  AMP PEAK 26(10Q22.2) WILD-TYPE   262
D26V6, multiclass
                                           clus
vv                                          AMP PEAK 26(10Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                           24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            4
  WHITE                                                               95
                                           clus
vv                                          AMP PEAK 26(10Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              5
  WHITE                                                                262
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(10Q22.2) MUTATED     3  95
  AMP PEAK 26(10Q22.2) WILD-TYPE  10 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(10Q22.2) MUTATED      3   95
  AMP PEAK 26(10Q22.2) WILD-TYPE   10  255
                        clus
vv                       AMP PEAK 26(10Q22.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           95
                        clus
vv                       AMP PEAK 26(10Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            255
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(11P11.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(11P11.2) MUTATED    38  10
  AMP PEAK 27(11P11.2) WILD-TYPE 405  50
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            48                            455 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            10                             50 
$`AMP PEAK 27(11P11.2) MUTATED`
TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3TW TCGA-AP-A053 
        7.33         1.08        22.26         0.92         1.71         5.95 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW 
       45.53        48.79        41.95        33.73        28.54        37.78 
TCGA-AX-A1C9 TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-B5-A0JT 
       15.25         4.77        19.36         2.96         0.03        43.13 
TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M2 
       17.88        50.89        11.87         5.03        34.95        20.94 
TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 
       36.49        24.39        15.45         6.81        10.22        67.20 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 
       49.55        22.55        37.32        11.51        18.67         6.77 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EY-A1GM TCGA-EY-A210 
       35.38        91.96        37.71        32.38         6.90        12.59 
TCGA-EY-A212 TCGA-EY-A72D TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A915 
        3.62         5.88        45.01         1.74        13.15         7.00 

$`AMP PEAK 27(11P11.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O 
       28.64         5.33         5.16        14.96         1.18         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
        0.76         1.94        15.95         1.87        16.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
        0.99         2.70         0.13        83.67        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       18.25         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.01        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       40.50        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       80.38        56.91        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        14.40        14.70        11.70        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 
       41.06        34.13        18.61        20.19        19.33        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98         7.92        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        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 
        6.21        10.16        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        23.47        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        88.34        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        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        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         1.41         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        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-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.01         7.36        16.80        10.92        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        24.79        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       13.97        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       29.10        27.35        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        6.97         3.72         5.29        40.01        34.98        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       36.00         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
        9.07        28.93        28.96        25.02        26.01        41.06 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
        2.43        10.82         9.11        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                         91.96                         191.84 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                        18.275                         23.340 
[1] "0.0 - 92.0 (18.3)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "2.3"
D27V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 27(11P11.2) MUTATED                                        16
  AMP PEAK 27(11P11.2) WILD-TYPE                                     364
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 27(11P11.2) MUTATED                               4
  AMP PEAK 27(11P11.2) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 27(11P11.2) MUTATED                                  28
  AMP PEAK 27(11P11.2) WILD-TYPE                                76
D27V3, multiclass
                                         clus
vv                                        AMP PEAK 27(11P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           16
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 28
                                         clus
vv                                        AMP PEAK 27(11P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            364
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V4, binary
                                cls
clus                               0   1
  AMP PEAK 27(11P11.2) MUTATED    12  36
  AMP PEAK 27(11P11.2) WILD-TYPE 126 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(11P11.2) MUTATED     12   36
  AMP PEAK 27(11P11.2) WILD-TYPE  126  331
     clus
vv    AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE
  NO                            12                            126
  YES                           36                            331
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(11P11.2) MUTATED    32   1   2   5
  AMP PEAK 27(11P11.2) WILD-TYPE 319  21  15  25
D27V5, multiclass
    clus
vv   AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE
  R0                           32                            319
  R1                            1                             21
  R2                            2                             15
  RX                            5                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(11P11.2) MUTATED                                  0     1
  AMP PEAK 27(11P11.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(11P11.2) MUTATED                          12
  AMP PEAK 27(11P11.2) WILD-TYPE                        78
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 27(11P11.2) MUTATED                                           2
  AMP PEAK 27(11P11.2) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 27(11P11.2) MUTATED      31
  AMP PEAK 27(11P11.2) WILD-TYPE   326
D27V6, multiclass
                                           clus
vv                                          AMP PEAK 27(11P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           12
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               31
                                           clus
vv                                          AMP PEAK 27(11P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             78
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(11P11.2) MUTATED     2  30
  AMP PEAK 27(11P11.2) WILD-TYPE  11 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(11P11.2) MUTATED      2   30
  AMP PEAK 27(11P11.2) WILD-TYPE   11  320
                        clus
vv                       AMP PEAK 27(11P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       AMP PEAK 27(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            320
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(11Q13.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 28(11Q13.2) MUTATED    55  12
  AMP PEAK 28(11Q13.2) WILD-TYPE 388  48
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            67                            436 
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            12                             48 
$`AMP PEAK 28(11Q13.2) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       65.75        11.44        36.33         7.33         1.18         1.08 
TCGA-AJ-A2QK TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L8 
        0.39         0.92         0.76        39.42        36.89        48.79 
TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       33.73        53.92        37.78        19.20        15.25        20.28 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FX 
        4.77        30.12        71.24        19.36         2.96         0.13 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0JX 
       20.52         0.03         0.23        80.38        43.13        44.71 
TCGA-B5-A0K4 TCGA-B5-A11Q TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 
       17.88        32.09        50.89        12.79        78.81         5.03 
TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0VT TCGA-BG-A18C TCGA-BK-A26L 
       20.94        36.49        41.52        24.39        15.45        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S 
       16.64        67.20        29.95        37.32        11.51        18.67 
TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1O0 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A8L9 
        1.41        28.08         2.07        35.38        31.10        24.33 
TCGA-EO-A1Y7 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A210 TCGA-EY-A212 
       18.81        16.34         4.54        23.90        12.59         3.62 
TCGA-EY-A2OQ TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A3PX TCGA-K6-A3WQ 
       29.10         5.88        34.98         9.07        45.01        13.15 
TCGA-PG-A914 
       12.92 

$`AMP PEAK 28(11Q13.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.96         1.97        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.49         1.12         0.76         2.24         1.68         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         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.71         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D 
       21.99         5.95        23.31        86.07         8.22        57.80 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       45.53         7.86        12.20        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        18.25         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CE 
       65.88        13.28        16.96        13.55        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       11.08        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.10         0.33         0.20         0.13         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47         0.13        56.91        46.75        48.76        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        36.82        33.50        27.35        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD 
      116.25        96.30        62.14        33.11        41.06        34.13 
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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MI 
        7.92        38.37        28.27        10.72        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        10.16        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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        19.79         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-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-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 
        6.77         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        12.39        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        22.26         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
        8.15        24.36        27.16        23.34        23.34        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33        14.40        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        27.35        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         3.72         5.29        40.01        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY 
        7.99        13.84         8.98        96.69        59.01        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        41.06         1.74         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       10.82         9.11        23.97         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                         80.38                         191.84 
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                         20.28                          23.11 
[1] "0.0 - 80.4 (20.3)"  "0.1 - 191.8 (23.1)"
[1] "hr=" "1.9"
D28V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 28(11Q13.2) MUTATED                                        31
  AMP PEAK 28(11Q13.2) WILD-TYPE                                     349
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 28(11Q13.2) MUTATED                               3
  AMP PEAK 28(11Q13.2) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 28(11Q13.2) MUTATED                                  33
  AMP PEAK 28(11Q13.2) WILD-TYPE                                71
D28V3, multiclass
                                         clus
vv                                        AMP PEAK 28(11Q13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           31
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 33
                                         clus
vv                                        AMP PEAK 28(11Q13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            349
  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"
D28V4, binary
                                cls
clus                               0   1
  AMP PEAK 28(11Q13.2) MUTATED    16  51
  AMP PEAK 28(11Q13.2) WILD-TYPE 122 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(11Q13.2) MUTATED     16   51
  AMP PEAK 28(11Q13.2) WILD-TYPE  122  316
     clus
vv    AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE
  NO                            16                            122
  YES                           51                            316
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(11Q13.2) MUTATED    40   2   4   6
  AMP PEAK 28(11Q13.2) WILD-TYPE 311  20  13  24
D28V5, multiclass
    clus
vv   AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE
  R0                           40                            311
  R1                            2                             20
  R2                            4                             13
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 28(11Q13.2) MUTATED                                  0     1
  AMP PEAK 28(11Q13.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(11Q13.2) MUTATED                          15
  AMP PEAK 28(11Q13.2) WILD-TYPE                        75
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 28(11Q13.2) MUTATED                                           1
  AMP PEAK 28(11Q13.2) WILD-TYPE                                         8
                                vv
clus                             WHITE
  AMP PEAK 28(11Q13.2) MUTATED      47
  AMP PEAK 28(11Q13.2) WILD-TYPE   310
D28V6, multiclass
                                           clus
vv                                          AMP PEAK 28(11Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               47
                                           clus
vv                                          AMP PEAK 28(11Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                310
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(11Q13.2) MUTATED     1  46
  AMP PEAK 28(11Q13.2) WILD-TYPE  12 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(11Q13.2) MUTATED      1   46
  AMP PEAK 28(11Q13.2) WILD-TYPE   12  304
                        clus
vv                       AMP PEAK 28(11Q13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       AMP PEAK 28(11Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            304
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(11Q14.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 29(11Q14.1) MUTATED    40  14
  AMP PEAK 29(11Q14.1) WILD-TYPE 403  46
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            54                            449 
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            14                             46 
$`AMP PEAK 29(11Q14.1) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A3BF 
       37.02        65.75        36.33         7.33         1.08         1.12 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AP-A5FX TCGA-AX-A0IW 
        0.92         0.76         1.71        48.79        33.73        37.78 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3G1 
       20.28        12.43         4.77        30.12         2.96        20.52 
TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K4 
        0.03         0.13        80.38        43.13        44.71        17.88 
TCGA-B5-A11Q TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-BG-A0M2 
       32.09       102.31        50.89        12.79        33.11        20.94 
TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A4ZD 
       36.49        41.52        24.39        15.45         6.81        16.64 
TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16V TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-DI-A1NN 
       67.20        11.51         1.41        18.25         2.07        35.38 
TCGA-DI-A2QT TCGA-EO-A1Y5 TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A212 TCGA-EY-A2OQ 
       12.39        10.92        22.26        23.90         3.62        29.10 
TCGA-EY-A4KR TCGA-FI-A2EY TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A914 TCGA-PG-A915 
        6.44        28.93        45.01        13.15        12.92         7.00 

$`AMP PEAK 29(11Q14.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        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         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
       14.96         1.18         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40         3.02         0.49         0.76         2.24         1.68 
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         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       16.96        13.55        15.25        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39        11.08        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        27.32        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.10         0.33         0.13         0.20         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18         8.35        14.47        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       40.67        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       23.01        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11R TCGA-B5-A11S 
       45.90        43.96        40.50        36.82        33.50        27.35 
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-A1MY TCGA-B5-A1MZ 
      191.84        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14         5.03        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 
       34.13        34.95        18.61        20.19        19.33        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG 
       34.98         7.92        38.37        28.27        10.72        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
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         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
       10.22        10.16        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        23.47        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        88.34        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        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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         6.77         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-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
        8.48        44.88         0.26         4.27         4.11        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30         9.37        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       24.33        16.01         7.36        16.80        18.81        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        26.96        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
        8.15        24.36        27.16        23.34        23.34        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        12.59        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        27.35        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        6.97         3.72         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.07        28.96        25.02        26.01        41.06 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 
        1.74         2.43        10.82         9.11        23.97        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                        102.31                         191.84 
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                        19.265                         23.310 
[1] "0.0 - 102.3 (19.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "3"  
D29V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 29(11Q14.1) MUTATED                                        20
  AMP PEAK 29(11Q14.1) WILD-TYPE                                     360
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 29(11Q14.1) MUTATED                               1
  AMP PEAK 29(11Q14.1) WILD-TYPE                            20
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 29(11Q14.1) MUTATED                                  33
  AMP PEAK 29(11Q14.1) WILD-TYPE                                71
D29V3, multiclass
                                         clus
vv                                        AMP PEAK 29(11Q14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           20
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 33
                                         clus
vv                                        AMP PEAK 29(11Q14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            360
  MIXED SEROUS AND ENDOMETRIOID                                       20
  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"
D29V4, binary
                                cls
clus                               0   1
  AMP PEAK 29(11Q14.1) MUTATED    10  44
  AMP PEAK 29(11Q14.1) WILD-TYPE 128 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(11Q14.1) MUTATED     10   44
  AMP PEAK 29(11Q14.1) WILD-TYPE  128  323
     clus
vv    AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE
  NO                            10                            128
  YES                           44                            323
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 29(11Q14.1) MUTATED    33   1   3   5
  AMP PEAK 29(11Q14.1) WILD-TYPE 318  21  14  25
D29V5, multiclass
    clus
vv   AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE
  R0                           33                            318
  R1                            1                             21
  R2                            3                             14
  RX                            5                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 29(11Q14.1) MUTATED                                  1     0
  AMP PEAK 29(11Q14.1) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(11Q14.1) MUTATED                          14
  AMP PEAK 29(11Q14.1) WILD-TYPE                        76
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 29(11Q14.1) MUTATED                                           1
  AMP PEAK 29(11Q14.1) WILD-TYPE                                         8
                                vv
clus                             WHITE
  AMP PEAK 29(11Q14.1) MUTATED      35
  AMP PEAK 29(11Q14.1) WILD-TYPE   322
D29V6, multiclass
                                           clus
vv                                          AMP PEAK 29(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               35
                                           clus
vv                                          AMP PEAK 29(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                322
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                               0   1
  AMP PEAK 29(11Q14.1) MUTATED     1  36
  AMP PEAK 29(11Q14.1) WILD-TYPE  12 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(11Q14.1) MUTATED      1   36
  AMP PEAK 29(11Q14.1) WILD-TYPE   12  314
                        clus
vv                       AMP PEAK 29(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       AMP PEAK 29(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            314
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(12P12.1) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 30(12P12.1) MUTATED    77   9
  AMP PEAK 30(12P12.1) WILD-TYPE 366  51
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            86                            417 
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                             9                             51 
$`AMP PEAK 30(12P12.1) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 
      149.56       105.37        17.59        11.44        36.33        46.32 
TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW 
        1.18         0.49         1.12         0.92         0.76         1.71 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A05W 
       20.91       125.42        31.30        41.95        16.24        68.35 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HA 
       37.78        65.88        20.28        11.08         4.77        68.71 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
       19.36         2.96         0.03         0.13        80.38        23.01 
TCGA-B5-A0K8 TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A1MY TCGA-B5-A1N2 
       17.85        33.50        19.56        19.50        11.87        12.79 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0M2 TCGA-BG-A0M6 TCGA-BG-A0M8 
        5.03        41.06        34.13        20.94         7.92        36.49 
TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 
       48.56        52.83        15.45        23.70         6.81        10.16 
TCGA-BK-A13B TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A168 
       31.76         4.80        61.87        67.20        63.58        36.10 
TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A17K TCGA-D1-A17U TCGA-D1-A1O0 TCGA-D1-A2G5 
       11.51        33.63        28.08        22.92         2.07        41.42 
TCGA-D1-A3DH TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
        4.11        24.30        35.38        91.96        48.36        24.33 
TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GC 
       10.92        32.38        35.15        27.16        26.96         4.54 
TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A3L3 
       19.27        15.09        19.33        12.59        14.40        27.35 
TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EY TCGA-FI-A3PX TCGA-K6-A3WQ 
        5.88        36.00         8.98        28.93        45.01        13.15 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`AMP PEAK 30(12P12.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
       42.35        15.95         7.92         9.60         8.02        91.04 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33        14.96         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         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         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87        16.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        39.42        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
        7.86        12.20        48.79       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DR 
       25.08        71.67        60.36        55.89        35.54        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       43.82        40.11        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       67.50        25.12        36.39        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       61.18        33.40        40.50        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        36.82        32.09        27.35        16.73 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU 
       18.41        17.36        16.57       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.40        14.70        11.70        15.29       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        33.11        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        34.98        38.37        28.27        10.72 
TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       41.52        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       34.29        52.64        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       35.67        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        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-A0TG 
        9.86        46.95        23.47        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        88.34        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        62.79 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-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-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       31.07        10.65         0.69        18.67         1.41         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         6.77 
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-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33         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         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62         9.37        12.39        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37         6.67        16.01         7.36        16.80        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3KU 
       24.79        19.40        34.39        19.36        12.89        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        17.62        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        8.55         6.48         3.62        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       45.76        31.04        29.10        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         3.72         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       33.99         7.99        13.84        96.69        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        41.06         1.74         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       10.82         9.11        23.97        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                        149.56                         191.84 
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                        20.925                         23.210 
[1] "0.0 - 149.6 (20.9)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.2"
D30V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 30(12P12.1) MUTATED                                        41
  AMP PEAK 30(12P12.1) WILD-TYPE                                     339
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 30(12P12.1) MUTATED                               4
  AMP PEAK 30(12P12.1) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 30(12P12.1) MUTATED                                  41
  AMP PEAK 30(12P12.1) WILD-TYPE                                63
D30V3, multiclass
                                         clus
vv                                        AMP PEAK 30(12P12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           41
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 41
                                         clus
vv                                        AMP PEAK 30(12P12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            339
  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"
D30V4, binary
                                cls
clus                               0   1
  AMP PEAK 30(12P12.1) MUTATED    20  66
  AMP PEAK 30(12P12.1) WILD-TYPE 118 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(12P12.1) MUTATED     20   66
  AMP PEAK 30(12P12.1) WILD-TYPE  118  301
     clus
vv    AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE
  NO                            20                            118
  YES                           66                            301
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 30(12P12.1) MUTATED    62   2   3   3
  AMP PEAK 30(12P12.1) WILD-TYPE 289  20  14  27
D30V5, multiclass
    clus
vv   AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE
  R0                           62                            289
  R1                            2                             20
  R2                            3                             14
  RX                            3                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 30(12P12.1) MUTATED                                  0     6
  AMP PEAK 30(12P12.1) WILD-TYPE                                4    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(12P12.1) MUTATED                          21
  AMP PEAK 30(12P12.1) WILD-TYPE                        69
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 30(12P12.1) MUTATED                                           2
  AMP PEAK 30(12P12.1) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 30(12P12.1) MUTATED      53
  AMP PEAK 30(12P12.1) WILD-TYPE   304
D30V6, multiclass
                                           clus
vv                                          AMP PEAK 30(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               53
                                           clus
vv                                          AMP PEAK 30(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             69
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                304
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(12P12.1) MUTATED     0  62
  AMP PEAK 30(12P12.1) WILD-TYPE  13 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(12P12.1) MUTATED      0   62
  AMP PEAK 30(12P12.1) WILD-TYPE   13  288
                        clus
vv                       AMP PEAK 30(12P12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK 30(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            288
[1] 2 2
[1] FALSE

Clustering(31) Variable = AMP PEAK 31(12Q13.11) MUTATION ANALYSIS
D31V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 31(12Q13.11) MUTATED    73   8
  AMP PEAK 31(12Q13.11) WILD-TYPE 370  52
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             81                             422 
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                              8                              52 
$`AMP PEAK 31(12Q13.11) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
      149.56        37.02       105.37        17.59        11.44        36.33 
TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3TW 
       46.32         1.18         0.49         1.12        22.26         1.71 
TCGA-AP-A053 TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1E4 
        5.95        20.91       125.42        97.71        31.30        16.24 
TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 
       68.35        37.78        65.88        20.28        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G3 
       30.12        61.18        68.71         2.96         0.20         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11R TCGA-B5-A11V 
        0.13         0.23         0.13        23.01        33.50        19.56 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MG 
       12.79         5.03        41.06        20.94        36.49        48.56 
TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 
       52.83        15.45        23.70         6.81         4.80        67.20 
TCGA-BS-A0V7 TCGA-D1-A0ZP TCGA-D1-A16O TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G5 
       63.58        29.95        33.63        18.67         2.07        41.42 
TCGA-D1-A2G7 TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
       44.88        24.30        35.38        12.39        91.96        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EY-A1GJ TCGA-EY-A1GM 
       24.33        18.81        32.38        35.15        23.90         6.90 
TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A3L3 
       19.27        17.62        19.33        12.59        14.40        27.35 
TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A3PX 
        6.44        36.00         8.98        59.01        28.93        45.01 
TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       13.15        23.97        12.92 

$`AMP PEAK 31(12Q13.11) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 
       15.95         7.92         9.60         8.02        91.04        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33        14.96         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79         0.85         2.40         3.02         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        2.24         1.68         1.64        14.66        22.49         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87        16.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
        8.22        39.42        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD 
       25.12        36.39        71.24        33.53        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G8 
        0.23         0.10         0.33         0.13        20.52         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       32.09        27.35        16.73        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        11.87        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        35.21        34.98         7.92        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       10.72        41.52        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        52.64        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
        9.57        35.67        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 
        6.21        10.22        10.16        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        23.47 
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        88.34        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        62.79        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         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         6.77         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         3.52         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26         4.27         4.11        27.16        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        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        6.67        16.01         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 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       19.40        34.39        19.36        12.89        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        8.55         6.48         3.62        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        29.10        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        6.97         3.72         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 
       33.99         7.99        13.84        96.69         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC 
       25.02        26.01        41.06         1.74         2.43        10.82 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        9.11         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                         149.56                          191.84 
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                          23.01                           22.80 
[1] "0.0 - 149.6 (23.0)" "0.1 - 191.8 (22.8)"
[1] "hr=" "1.3"
D31V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 31(12Q13.11) MUTATED                                        38
  AMP PEAK 31(12Q13.11) WILD-TYPE                                     342
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 31(12Q13.11) MUTATED                               4
  AMP PEAK 31(12Q13.11) WILD-TYPE                            17
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 31(12Q13.11) MUTATED                                  39
  AMP PEAK 31(12Q13.11) WILD-TYPE                                65
D31V3, multiclass
                                         clus
vv                                        AMP PEAK 31(12Q13.11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            38
  MIXED SEROUS AND ENDOMETRIOID                                       4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  39
                                         clus
vv                                        AMP PEAK 31(12Q13.11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             342
  MIXED SEROUS AND ENDOMETRIOID                                        17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                                 cls
clus                                0   1
  AMP PEAK 31(12Q13.11) MUTATED    16  65
  AMP PEAK 31(12Q13.11) WILD-TYPE 122 302
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(12Q13.11) MUTATED     16   65
  AMP PEAK 31(12Q13.11) WILD-TYPE  122  302
     clus
vv    AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE
  NO                             16                             122
  YES                            65                             302
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 31(12Q13.11) MUTATED    56   2   5   5
  AMP PEAK 31(12Q13.11) WILD-TYPE 295  20  12  25
D31V5, multiclass
    clus
vv   AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE
  R0                            56                             295
  R1                             2                              20
  R2                             5                              12
  RX                             5                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 31(12Q13.11) MUTATED                                  1     6
  AMP PEAK 31(12Q13.11) WILD-TYPE                                3    13
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(12Q13.11) MUTATED                          22
  AMP PEAK 31(12Q13.11) WILD-TYPE                        68
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 31(12Q13.11) MUTATED                                           3
  AMP PEAK 31(12Q13.11) WILD-TYPE                                         6
                                 vv
clus                              WHITE
  AMP PEAK 31(12Q13.11) MUTATED      47
  AMP PEAK 31(12Q13.11) WILD-TYPE   310
D31V6, multiclass
                                           clus
vv                                          AMP PEAK 31(12Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                47
                                           clus
vv                                          AMP PEAK 31(12Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  13
  BLACK OR AFRICAN AMERICAN                                              68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  WHITE                                                                 310
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                                 cls
clus                                0   1
  AMP PEAK 31(12Q13.11) MUTATED     1  59
  AMP PEAK 31(12Q13.11) WILD-TYPE  12 291
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(12Q13.11) MUTATED      1   59
  AMP PEAK 31(12Q13.11) WILD-TYPE   12  291
                        clus
vv                       AMP PEAK 31(12Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            59
                        clus
vv                       AMP PEAK 31(12Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             291
[1] 2 2
[1] FALSE

Clustering(32) Variable = AMP PEAK 32(12Q13.2) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 32(12Q13.2) MUTATED    83   9
  AMP PEAK 32(12Q13.2) WILD-TYPE 360  51
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            92                            411 
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                             9                             51 
$`AMP PEAK 32(12Q13.2) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
      149.56        37.02       105.37        36.82        19.96        17.59 
TCGA-A5-A1OG TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF 
       11.44        46.32        14.96         1.18         0.49         1.12 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05P 
       22.26         1.28         0.76        21.99        45.53        20.91 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A1DO TCGA-AP-A1E4 TCGA-AX-A05W 
      125.42         3.39        36.36        31.30        16.24        68.35 
TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
       37.78        65.88        16.96        13.55        20.28        12.43 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A3FW 
       11.08         4.77        30.12        68.71        19.36         0.33 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11R TCGA-B5-A11V 
        0.13        20.52        23.01        17.85        33.50        19.56 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MG 
        5.03        41.06        34.13        20.94        36.49        48.56 
TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A4ZD TCGA-BS-A0TE 
       52.83        15.45        23.70         6.81        16.64         4.80 
TCGA-BS-A0U9 TCGA-BS-A0V7 TCGA-D1-A16O TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G5 
       67.20        63.58        33.63        18.67         2.07        41.42 
TCGA-D1-A3DH TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
        4.11        24.30        35.38        12.39        91.96        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EY-A1GC 
       24.33        18.81        37.71        32.38        35.15         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       23.90        19.27        17.62        19.33        12.59        14.40 
TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D2 
       13.45        27.35        13.84         5.88        40.01        36.00 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
        8.98        59.01        26.01        45.01         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A7D5 
        2.43        23.97 

$`AMP PEAK 32(12Q13.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88        83.51        17.85        32.78         3.22 
TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN 
       87.32        74.10        57.53        65.75        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        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         7.92 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        0.85         2.40         3.02         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.71         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       71.67        60.36        55.89        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX 
        6.71        30.90        10.42        27.85        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z 
        0.56        13.58        19.82        29.69        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE 
       43.82        40.11        13.28        19.20        15.25        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        33.53        61.18        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.10         0.20         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       32.09        27.35        16.73        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        33.11        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        35.21        34.98         7.92        38.37        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ 
       10.72        41.52        23.47        43.30        43.04        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        52.64        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
        9.57        35.67        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 
        6.21        10.22        10.16        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        23.47        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        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        62.79        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         1.41         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         6.77         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         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        27.16        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        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
        6.67        16.01         7.36        16.80        10.92        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        24.79        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       34.39        19.36        12.89        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
        6.48         3.62        18.87        22.82        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       29.10         6.44        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU 
        5.29        34.98        33.99         7.99        13.84        96.69 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-PG-A5BC 
        9.07        28.93        28.96        25.02        41.06        10.82 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                        149.56                         191.84 
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                        20.715                         23.340 
[1] "0.1 - 149.6 (20.7)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.2"
D32V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 32(12Q13.2) MUTATED                                        47
  AMP PEAK 32(12Q13.2) WILD-TYPE                                     333
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 32(12Q13.2) MUTATED                               4
  AMP PEAK 32(12Q13.2) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 32(12Q13.2) MUTATED                                  41
  AMP PEAK 32(12Q13.2) WILD-TYPE                                63
D32V3, multiclass
                                         clus
vv                                        AMP PEAK 32(12Q13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           47
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 41
                                         clus
vv                                        AMP PEAK 32(12Q13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            333
  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"
D32V4, binary
                                cls
clus                               0   1
  AMP PEAK 32(12Q13.2) MUTATED    17  75
  AMP PEAK 32(12Q13.2) WILD-TYPE 121 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(12Q13.2) MUTATED     17   75
  AMP PEAK 32(12Q13.2) WILD-TYPE  121  292
     clus
vv    AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE
  NO                            17                            121
  YES                           75                            292
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(12Q13.2) MUTATED    67   3   7   3
  AMP PEAK 32(12Q13.2) WILD-TYPE 284  19  10  27
D32V5, multiclass
    clus
vv   AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE
  R0                           67                            284
  R1                            3                             19
  R2                            7                             10
  RX                            3                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 32(12Q13.2) MUTATED                                  1     6
  AMP PEAK 32(12Q13.2) WILD-TYPE                                3    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(12Q13.2) MUTATED                          23
  AMP PEAK 32(12Q13.2) WILD-TYPE                        67
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 32(12Q13.2) MUTATED                                           2
  AMP PEAK 32(12Q13.2) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 32(12Q13.2) MUTATED      56
  AMP PEAK 32(12Q13.2) WILD-TYPE   301
D32V6, multiclass
                                           clus
vv                                          AMP PEAK 32(12Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               56
                                           clus
vv                                          AMP PEAK 32(12Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                301
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                                cls
clus                               0   1
  AMP PEAK 32(12Q13.2) MUTATED     2  69
  AMP PEAK 32(12Q13.2) WILD-TYPE  11 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(12Q13.2) MUTATED      2   69
  AMP PEAK 32(12Q13.2) WILD-TYPE   11  281
                        clus
vv                       AMP PEAK 32(12Q13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK 32(12Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            281
[1] 2 2
[1] FALSE

Clustering(33) Variable = AMP PEAK 33(13Q34) MUTATION ANALYSIS
D33V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 33(13Q34) MUTATED    48   8
  AMP PEAK 33(13Q34) WILD-TYPE 395  52
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                          56                          447 
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                           8                           52 
$`AMP PEAK 33(13Q34) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A23N 
       37.02        11.44        36.33        28.64         1.18         1.08 
TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A1DV 
        0.92        16.87        48.79       125.42         3.39         6.71 
TCGA-AW-A1PO TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HF 
        0.56        20.28        11.08         4.77        71.24        19.36 
TCGA-AX-A2IO TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS 
       38.70         0.03        80.38        17.85        75.72       102.31 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BK-A26L TCGA-BS-A0TA TCGA-BS-A0V8 TCGA-D1-A15V 
        5.03        34.13        24.13        23.47        49.55        39.48 
TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1O0 
        0.66        11.51        18.67         0.72        16.87         2.07 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG 
       35.38        91.96        48.36        10.92        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A214 
       19.40        26.96        19.27        15.09        12.59        14.40 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2F9 TCGA-PG-A7D5 
       27.35         6.44         3.72        36.00        26.01        23.97 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`AMP PEAK 33(13Q34) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        91.04        46.32         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.96         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        3.02         0.49         1.12         0.76         2.24         1.68 
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         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65         1.35        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
        1.87         1.71         2.33         0.99         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       39.42        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       20.91       117.99       110.37        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1E0 
       55.89        31.30        35.54        41.95        49.15        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        18.25        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        30.12        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        68.71        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32         2.96        31.13         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.13         0.20        20.52         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47         0.13        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        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       191.84        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       78.81        62.14        33.11        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        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-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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        21.99        30.08        29.88         1.91 
TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         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         6.77         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-A1NZ 
        2.33        22.92         1.41        13.22        18.25        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        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-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        24.33        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        18.81        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       33.01        27.12        57.60        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        13.84        17.92         2.14         6.97 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        5.29         5.88        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        41.06        45.01         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        2.43        10.82         9.11        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                        0.03                         0.10 
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                      125.42                       191.84 
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                      19.315                       23.210 
[1] "0.0 - 125.4 (19.3)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.4"
D33V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 33(13Q34) MUTATED                                        14
  AMP PEAK 33(13Q34) WILD-TYPE                                     366
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 33(13Q34) MUTATED                               4
  AMP PEAK 33(13Q34) WILD-TYPE                            17
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 33(13Q34) MUTATED                                  38
  AMP PEAK 33(13Q34) WILD-TYPE                                66
D33V3, multiclass
                                         clus
vv                                        AMP PEAK 33(13Q34) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         14
  MIXED SEROUS AND ENDOMETRIOID                                    4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               38
                                         clus
vv                                        AMP PEAK 33(13Q34) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          366
  MIXED SEROUS AND ENDOMETRIOID                                     17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V4, binary
                              cls
clus                             0   1
  AMP PEAK 33(13Q34) MUTATED    15  41
  AMP PEAK 33(13Q34) WILD-TYPE 123 326
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(13Q34) MUTATED     15   41
  AMP PEAK 33(13Q34) WILD-TYPE  123  326
     clus
vv    AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE
  NO                          15                          123
  YES                         41                          326
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 33(13Q34) MUTATED    34   6   4   5
  AMP PEAK 33(13Q34) WILD-TYPE 317  16  13  25
D33V5, multiclass
    clus
vv   AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE
  R0                         34                          317
  R1                          6                           16
  R2                          4                           13
  RX                          5                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 33(13Q34) MUTATED                                  0     2
  AMP PEAK 33(13Q34) WILD-TYPE                                4    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(13Q34) MUTATED                          18
  AMP PEAK 33(13Q34) WILD-TYPE                        72
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(13Q34) MUTATED                                           2    30
  AMP PEAK 33(13Q34) WILD-TYPE                                         7   327
D33V6, multiclass
                                           clus
vv                                          AMP PEAK 33(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             30
                                           clus
vv                                          AMP PEAK 33(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  WHITE                                                              327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                              cls
clus                             0   1
  AMP PEAK 33(13Q34) MUTATED     1  36
  AMP PEAK 33(13Q34) WILD-TYPE  12 314
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(13Q34) MUTATED      1   36
  AMP PEAK 33(13Q34) WILD-TYPE   12  314
                        clus
vv                       AMP PEAK 33(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         36
                        clus
vv                       AMP PEAK 33(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          314
[1] 2 2
[1] FALSE

Clustering(34) Variable = AMP PEAK 34(14Q24.3) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 34(14Q24.3) MUTATED    44  15
  AMP PEAK 34(14Q24.3) WILD-TYPE 399  45
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            59                            444 
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            15                             45 
$`AMP PEAK 34(14Q24.3) MUTATED`
TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP 
       36.82        36.33         8.02        91.04        28.64        14.96 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AP-A053 TCGA-AP-A05A 
        1.64        22.26         0.92         1.35         5.95        39.42 
TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IW 
       36.89       125.42        97.71        41.95        18.25        37.78 
TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2HF TCGA-AX-A2IO TCGA-AX-A3FX 
       12.43        11.08        30.12        19.36        38.70         0.13 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A1MU TCGA-BG-A18C 
        0.13        56.91        23.01        17.88        50.89        15.45 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ 
        6.81        35.90        24.13        16.64        67.20        22.55 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 
       37.32        11.51         6.77        18.25         2.07        41.42 
TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3B1 TCGA-EY-A1GC 
       91.96        17.06        10.92        24.79        26.96         4.54 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
        8.55         3.62         6.44        36.00        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-PG-A7D5 
       28.93        26.01        41.06        13.15        23.97 

$`AMP PEAK 34(14Q24.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       65.75        60.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
        9.60        46.32         5.33         5.16         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.08         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        3.02         0.49         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49         1.28        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.76         1.94        15.95         1.87        16.87         1.71 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        2.33         0.99         2.70         0.13        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05N 
       23.31        86.07         8.22        57.80        45.53         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91        48.79       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        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        30.90        10.42        27.85        16.24        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        20.28        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       26.33        17.75        27.32         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.10         0.33         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JS 
        0.23         1.18         8.35        14.47        80.38        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       28.34        30.51        25.91        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84       102.31        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        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         6.21        10.22        10.16        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        23.47 
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        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         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-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         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        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-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       31.10        23.38        48.36         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.01         7.36        16.80        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU 
       34.39        19.36        35.15        12.89        27.16        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       27.35        13.84        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        5.29         5.88        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PX 
       13.84         8.98        96.69        28.96        25.02        45.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 
        1.74         2.43        10.82         9.11        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                        125.42                         191.84 
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                         22.55                          22.87 
[1] "0.1 - 125.4 (22.6)" "0.0 - 191.8 (22.9)"
[1] "hr=" "2.6"
D34V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 34(14Q24.3) MUTATED                                        20
  AMP PEAK 34(14Q24.3) WILD-TYPE                                     360
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 34(14Q24.3) MUTATED                               4
  AMP PEAK 34(14Q24.3) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 34(14Q24.3) MUTATED                                  35
  AMP PEAK 34(14Q24.3) WILD-TYPE                                69
D34V3, multiclass
                                         clus
vv                                        AMP PEAK 34(14Q24.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           20
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 35
                                         clus
vv                                        AMP PEAK 34(14Q24.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            360
  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"
D34V4, binary
                                cls
clus                               0   1
  AMP PEAK 34(14Q24.3) MUTATED    11  48
  AMP PEAK 34(14Q24.3) WILD-TYPE 127 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(14Q24.3) MUTATED     11   48
  AMP PEAK 34(14Q24.3) WILD-TYPE  127  319
     clus
vv    AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE
  NO                            11                            127
  YES                           48                            319
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 34(14Q24.3) MUTATED    40   4   2   6
  AMP PEAK 34(14Q24.3) WILD-TYPE 311  18  15  24
D34V5, multiclass
    clus
vv   AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE
  R0                           40                            311
  R1                            4                             18
  R2                            2                             15
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 34(14Q24.3) MUTATED                                  0     0
  AMP PEAK 34(14Q24.3) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 34(14Q24.3) MUTATED                           9
  AMP PEAK 34(14Q24.3) WILD-TYPE                        81
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 34(14Q24.3) MUTATED                                           1
  AMP PEAK 34(14Q24.3) WILD-TYPE                                         8
                                vv
clus                             WHITE
  AMP PEAK 34(14Q24.3) MUTATED      45
  AMP PEAK 34(14Q24.3) WILD-TYPE   312
D34V6, multiclass
                                           clus
vv                                          AMP PEAK 34(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               45
                                           clus
vv                                          AMP PEAK 34(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                312
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                cls
clus                               0   1
  AMP PEAK 34(14Q24.3) MUTATED     2  40
  AMP PEAK 34(14Q24.3) WILD-TYPE  11 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(14Q24.3) MUTATED      2   40
  AMP PEAK 34(14Q24.3) WILD-TYPE   11  310
                        clus
vv                       AMP PEAK 34(14Q24.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       AMP PEAK 34(14Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(35) Variable = AMP PEAK 35(14Q32.33) MUTATION ANALYSIS
D35V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 35(14Q32.33) MUTATED    58  13
  AMP PEAK 35(14Q32.33) WILD-TYPE 385  47
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             71                             432 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             13                              47 
$`AMP PEAK 35(14Q32.33) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 
       37.02        65.75        36.82        36.33         8.02        91.04 
TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3QS 
       28.64        14.96         1.12        22.26         0.92        16.87 
TCGA-AP-A05A TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       39.42        48.79        97.71        18.25        33.73         0.56 
TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A3FX 
       37.78        12.43        76.83        11.08        30.12         0.13 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0K4 TCGA-B5-A0KB TCGA-B5-A1MU 
        0.13        80.38        56.91        17.88         4.11        50.89 
TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0C9 
       33.11        34.95        36.49        15.45         6.81        35.90 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 
       24.13        16.64        67.20        49.55        22.55        37.32 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G7 TCGA-D1-A3DG 
       11.51        18.67         2.07        41.42        44.88         4.27 
TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3B1 
       91.96        17.06        18.81        37.71        24.79        26.96 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2ON 
        4.54        23.90         8.55        12.59         3.62        13.45 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       27.35         6.44         3.72        36.00        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A914 
       28.93        41.06         1.74        13.15        12.92 

$`AMP PEAK 35(14Q32.33) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        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-A2K3 
       42.35        15.95         7.92        11.44         9.60        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16         7.33         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        1.28        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        20.28        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       67.50        25.12        36.39         4.77        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.10         0.33         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JT 
        0.23         1.18         8.35        14.47        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        23.01        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        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       191.84       102.31        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       78.81        62.14         5.03        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       23.70        20.12        11.31        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.16        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        23.47        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        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         1.41         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         6.77 
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-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-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
        3.52         8.48         0.26         4.11        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-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       31.10        23.38        48.36         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S 
       16.01         7.36        16.80        10.92        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        57.60        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW 
       19.36        35.15        12.89        27.16        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
        6.48        19.33        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        13.84        17.92         2.14         6.97 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        5.29         5.88        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       13.84         8.98        96.69        28.96        25.02        26.01 
TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 
       45.01         2.43        10.82         9.11        23.97         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                           0.13                            0.03 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                          97.71                          191.84 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                           23.9                            22.8 
[1] "0.1 - 97.7 (23.9)"  "0.0 - 191.8 (22.8)"
[1] "hr=" "1.7"
D35V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 35(14Q32.33) MUTATED                                        29
  AMP PEAK 35(14Q32.33) WILD-TYPE                                     351
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 35(14Q32.33) MUTATED                               5
  AMP PEAK 35(14Q32.33) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 35(14Q32.33) MUTATED                                  38
  AMP PEAK 35(14Q32.33) WILD-TYPE                                66
D35V3, multiclass
                                         clus
vv                                        AMP PEAK 35(14Q32.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            29
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  38
                                         clus
vv                                        AMP PEAK 35(14Q32.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             351
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                                 cls
clus                                0   1
  AMP PEAK 35(14Q32.33) MUTATED    11  61
  AMP PEAK 35(14Q32.33) WILD-TYPE 127 306
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(14Q32.33) MUTATED     11   61
  AMP PEAK 35(14Q32.33) WILD-TYPE  127  306
     clus
vv    AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE
  NO                             11                             127
  YES                            61                             306
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 35(14Q32.33) MUTATED    46   4   4   7
  AMP PEAK 35(14Q32.33) WILD-TYPE 305  18  13  23
D35V5, multiclass
    clus
vv   AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE
  R0                            46                             305
  R1                             4                              18
  R2                             4                              13
  RX                             7                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 35(14Q32.33) MUTATED                                  0     0
  AMP PEAK 35(14Q32.33) WILD-TYPE                                4    19
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 35(14Q32.33) MUTATED                          22
  AMP PEAK 35(14Q32.33) WILD-TYPE                        68
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 35(14Q32.33) MUTATED                                           2
  AMP PEAK 35(14Q32.33) WILD-TYPE                                         7
                                 vv
clus                              WHITE
  AMP PEAK 35(14Q32.33) MUTATED      43
  AMP PEAK 35(14Q32.33) WILD-TYPE   314
D35V6, multiclass
                                           clus
vv                                          AMP PEAK 35(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 0
  BLACK OR AFRICAN AMERICAN                                            22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                                43
                                           clus
vv                                          AMP PEAK 35(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  19
  BLACK OR AFRICAN AMERICAN                                              68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               7
  WHITE                                                                 314
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                                 cls
clus                                0   1
  AMP PEAK 35(14Q32.33) MUTATED     1  51
  AMP PEAK 35(14Q32.33) WILD-TYPE  12 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(14Q32.33) MUTATED      1   51
  AMP PEAK 35(14Q32.33) WILD-TYPE   12  299
                        clus
vv                       AMP PEAK 35(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            51
                        clus
vv                       AMP PEAK 35(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             299
[1] 2 2
[1] FALSE

Clustering(36) Variable = AMP PEAK 36(15Q26.3) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 36(15Q26.3) MUTATED    28   8
  AMP PEAK 36(15Q26.3) WILD-TYPE 415  52
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            36                            467 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                             8                             52 
$`AMP PEAK 36(15Q26.3) MUTATED`
TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A1C7 
        0.49         0.92         0.76        97.71        41.95        16.96 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF 
       76.83        11.08        30.12        61.18        40.50        19.36 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A11I TCGA-BG-A0M8 TCGA-BK-A0CC TCGA-BS-A0TE 
        0.13        20.52        75.72        36.49        10.22         4.80 
TCGA-D1-A102 TCGA-D1-A16G TCGA-D1-A17K TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1M0 
        4.44        27.42        28.08        35.38        91.96        17.06 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A72D TCGA-FI-A2CX 
       32.38        34.39         4.54         8.55         5.88        40.01 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A5BC TCGA-PG-A914 
       28.93        41.06        45.01         1.74        10.82        12.92 

$`AMP PEAK 36(15Q26.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       28.64         5.33         5.16         7.33        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.08         1.97         0.39        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         1.12         0.76         2.24         1.68         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         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.71         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       21.99         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        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 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        13.55        15.25        20.28        12.43        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH 
       71.24        33.53        68.71        33.40        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.33         0.20         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
        5.03        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
        6.21        10.16        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        23.47        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        67.20        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        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-A16I TCGA-D1-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        11.51        29.92        31.07 
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         1.41         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         6.77 
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-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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 
        9.37        12.39        31.10        23.38        48.36         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       18.81        37.71        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        24.79        19.40        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       13.45        45.76        31.04        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.07        28.96        25.02        26.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 
       13.15         2.43         9.11        23.97         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                         97.71                         191.84 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                         23.97                          22.82 
[1] "0.1 - 97.7 (24.0)"  "0.0 - 191.8 (22.8)"
[1] "hr=" "2.2"
D36V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 36(15Q26.3) MUTATED                                        17
  AMP PEAK 36(15Q26.3) WILD-TYPE                                     363
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 36(15Q26.3) MUTATED                               1
  AMP PEAK 36(15Q26.3) WILD-TYPE                            20
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 36(15Q26.3) MUTATED                                  18
  AMP PEAK 36(15Q26.3) WILD-TYPE                                86
D36V3, multiclass
                                         clus
vv                                        AMP PEAK 36(15Q26.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           17
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 18
                                         clus
vv                                        AMP PEAK 36(15Q26.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            363
  MIXED SEROUS AND ENDOMETRIOID                                       20
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V4, binary
                                cls
clus                               0   1
  AMP PEAK 36(15Q26.3) MUTATED     5  31
  AMP PEAK 36(15Q26.3) WILD-TYPE 133 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(15Q26.3) MUTATED      5   31
  AMP PEAK 36(15Q26.3) WILD-TYPE  133  336
     clus
vv    AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE
  NO                             5                            133
  YES                           31                            336
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 36(15Q26.3) MUTATED    20   3   4   4
  AMP PEAK 36(15Q26.3) WILD-TYPE 331  19  13  26
D36V5, multiclass
    clus
vv   AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE
  R0                           20                            331
  R1                            3                             19
  R2                            4                             13
  RX                            4                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 36(15Q26.3) MUTATED                                  0     2
  AMP PEAK 36(15Q26.3) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(15Q26.3) MUTATED                           8
  AMP PEAK 36(15Q26.3) WILD-TYPE                        82
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 36(15Q26.3) MUTATED                                           0
  AMP PEAK 36(15Q26.3) WILD-TYPE                                         9
                                vv
clus                             WHITE
  AMP PEAK 36(15Q26.3) MUTATED      25
  AMP PEAK 36(15Q26.3) WILD-TYPE   332
D36V6, multiclass
                                           clus
vv                                          AMP PEAK 36(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            8
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               25
                                           clus
vv                                          AMP PEAK 36(15Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             82
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              9
  WHITE                                                                332
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                                cls
clus                               0   1
  AMP PEAK 36(15Q26.3) MUTATED     2  30
  AMP PEAK 36(15Q26.3) WILD-TYPE  11 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(15Q26.3) MUTATED      2   30
  AMP PEAK 36(15Q26.3) WILD-TYPE   11  320
                        clus
vv                       AMP PEAK 36(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       AMP PEAK 36(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            320
[1] 2 2
[1] FALSE

Clustering(37) Variable = AMP PEAK 37(16P11.2) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 37(16P11.2) MUTATED    48  14
  AMP PEAK 37(16P11.2) WILD-TYPE 395  46
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            62                            441 
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            14                             46 
$`AMP PEAK 37(16P11.2) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD 
       65.75        11.44        91.04        14.96         1.08         0.49 
TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IU 
       21.99        57.80        36.89        41.95        18.25        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A2H5 TCGA-AX-A3G1 TCGA-AX-A3GI 
       37.78        16.96        20.28        71.24        20.52         0.13 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MY 
       80.38        17.85        75.72        19.56       102.31        11.87 
TCGA-B5-A1N2 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A3PP TCGA-BK-A0CC 
       12.79         7.92        36.49        24.39         6.81        10.22 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A102 TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16I 
       24.13        67.20         4.44        36.10        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH 
       29.92        18.67        28.08         0.72        18.25         4.11 
TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU 
       31.10        18.81        37.71        32.38        19.40        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A3L3 
       16.34         4.54         8.55         3.62        29.10        27.35 
TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A3PX TCGA-PG-A7D5 
       17.92         3.72         5.88        36.00        45.01        23.97 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`AMP PEAK 37(16P11.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        7.33         1.18         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40         3.02         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65         1.35        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95         1.87        16.87         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        39.42        45.53         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        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        30.90        10.42        27.85        16.24        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 
        0.23         0.10         0.33         0.13         0.20         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.13         0.23         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        11.01         4.11         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W 
       36.82        32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        33.11         5.03        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        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       15.42        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
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         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        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-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         1.41         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         6.77 
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-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41        13.22        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48        44.88         0.26         4.27        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-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
       24.33        16.01         7.36        16.80        10.92        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       35.05        33.01        27.12        57.60        24.79        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 
       19.36        35.15        12.89        27.16        26.96         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       13.45        45.76        31.04        13.84         6.44         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        6.97         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        26.01        41.06         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        2.43        10.82         9.11        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                        102.31                         191.84 
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                         19.92                          23.31 
[1] "0.1 - 102.3 (19.9)" "0.0 - 191.8 (23.3)"
[1] "hr=" "2.4"
D37V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 37(16P11.2) MUTATED                                        20
  AMP PEAK 37(16P11.2) WILD-TYPE                                     360
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 37(16P11.2) MUTATED                               2
  AMP PEAK 37(16P11.2) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 37(16P11.2) MUTATED                                  40
  AMP PEAK 37(16P11.2) WILD-TYPE                                64
D37V3, multiclass
                                         clus
vv                                        AMP PEAK 37(16P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           20
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 40
                                         clus
vv                                        AMP PEAK 37(16P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            360
  MIXED SEROUS AND ENDOMETRIOID                                       19
  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"
D37V4, binary
                                cls
clus                               0   1
  AMP PEAK 37(16P11.2) MUTATED    14  48
  AMP PEAK 37(16P11.2) WILD-TYPE 124 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(16P11.2) MUTATED     14   48
  AMP PEAK 37(16P11.2) WILD-TYPE  124  319
     clus
vv    AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE
  NO                            14                            124
  YES                           48                            319
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 37(16P11.2) MUTATED    40   3   3   8
  AMP PEAK 37(16P11.2) WILD-TYPE 311  19  14  22
D37V5, multiclass
    clus
vv   AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE
  R0                           40                            311
  R1                            3                             19
  R2                            3                             14
  RX                            8                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 37(16P11.2) MUTATED                                  0     2
  AMP PEAK 37(16P11.2) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 37(16P11.2) MUTATED                          18
  AMP PEAK 37(16P11.2) WILD-TYPE                        72
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 37(16P11.2) MUTATED                                           1
  AMP PEAK 37(16P11.2) WILD-TYPE                                         8
                                vv
clus                             WHITE
  AMP PEAK 37(16P11.2) MUTATED      36
  AMP PEAK 37(16P11.2) WILD-TYPE   321
D37V6, multiclass
                                           clus
vv                                          AMP PEAK 37(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               36
                                           clus
vv                                          AMP PEAK 37(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                                cls
clus                               0   1
  AMP PEAK 37(16P11.2) MUTATED     2  44
  AMP PEAK 37(16P11.2) WILD-TYPE  11 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(16P11.2) MUTATED      2   44
  AMP PEAK 37(16P11.2) WILD-TYPE   11  306
                        clus
vv                       AMP PEAK 37(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       AMP PEAK 37(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            306
[1] 2 2
[1] FALSE

Clustering(38) Variable = AMP PEAK 38(17Q11.2) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 38(17Q11.2) MUTATED    56  12
  AMP PEAK 38(17Q11.2) WILD-TYPE 387  48
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            68                            435 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            12                             48 
$`AMP PEAK 38(17Q11.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 
       37.02        17.59        11.44        36.33        91.04        28.64 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS 
       14.96         1.18         0.49         1.64         0.76        16.87 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0LI TCGA-AP-A5FX TCGA-AX-A1C4 
       39.42        57.80        36.89        97.71        33.73        13.28 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       16.96        13.55        36.39         4.77        30.12        71.24 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0KB 
       17.75         2.96         0.23         0.13        23.01         4.11 
TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-BG-A0M4 
       75.72        11.87        12.79        78.81         5.03        34.98 
TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP 
       12.56         6.81        10.22        67.20        49.55        29.95 
TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DA TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
        0.72         2.07         0.26        35.38        12.39        91.96 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GJ 
       24.33        10.92        19.40        26.96        16.34        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ 
        6.90        19.27        15.09        12.59        13.45        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A3PX TCGA-K6-A3WQ 
       13.84         6.44        36.00         9.07        45.01        13.15 
TCGA-KJ-A3U4 TCGA-PG-A915 
        2.43         7.00 

$`AMP PEAK 38(17Q11.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        23.21        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A23O 
       46.32         5.33         5.16         7.33         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76         2.24         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        45.53         7.86        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       48.79       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        18.25 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 
       28.54        37.78        43.82        40.11        65.88        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2H8 
       54.12        67.50        25.12        11.08        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       68.71        33.40        40.50        19.36        26.33        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.03         0.13         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       25.91        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC 
       15.29       116.25        96.30        62.14        33.11        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21         7.92        38.37        36.49        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        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-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        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         6.21        10.16        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 
       23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       63.58        63.16        66.48        16.83        19.79         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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-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 
        1.41         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         6.77         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-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DG 
        3.95         3.52        41.42         8.48        44.88         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        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        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        6.67        16.01         7.36        16.80        18.81        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       32.38        34.39        19.36        35.15        12.89        27.16 
TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP 
       27.16        23.34        23.34        22.78        13.97        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        17.62        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33         3.62        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04        27.35        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        3.72         5.29         5.88        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY 
        7.99        13.84         8.98        96.69        59.01        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A5BC 
       28.96        25.02        26.01        41.06         1.74        10.82 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                         97.71                         191.84 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                        15.715                         23.470 
[1] "0.1 - 97.7 (15.7)"  "0.0 - 191.8 (23.5)"
[1] "hr=" "2"  
D38V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 38(17Q11.2) MUTATED                                        16
  AMP PEAK 38(17Q11.2) WILD-TYPE                                     364
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 38(17Q11.2) MUTATED                               6
  AMP PEAK 38(17Q11.2) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 38(17Q11.2) MUTATED                                  46
  AMP PEAK 38(17Q11.2) WILD-TYPE                                58
D38V3, multiclass
                                         clus
vv                                        AMP PEAK 38(17Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           16
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 46
                                         clus
vv                                        AMP PEAK 38(17Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            364
  MIXED SEROUS AND ENDOMETRIOID                                       15
  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"
D38V4, binary
                                cls
clus                               0   1
  AMP PEAK 38(17Q11.2) MUTATED    15  53
  AMP PEAK 38(17Q11.2) WILD-TYPE 123 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(17Q11.2) MUTATED     15   53
  AMP PEAK 38(17Q11.2) WILD-TYPE  123  314
     clus
vv    AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE
  NO                            15                            123
  YES                           53                            314
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 38(17Q11.2) MUTATED    38   7   6   6
  AMP PEAK 38(17Q11.2) WILD-TYPE 313  15  11  24
D38V5, multiclass
    clus
vv   AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE
  R0                           38                            313
  R1                            7                             15
  R2                            6                             11
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 38(17Q11.2) MUTATED                                  1     1
  AMP PEAK 38(17Q11.2) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 38(17Q11.2) MUTATED                          22
  AMP PEAK 38(17Q11.2) WILD-TYPE                        68
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 38(17Q11.2) MUTATED                                           2
  AMP PEAK 38(17Q11.2) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 38(17Q11.2) MUTATED      38
  AMP PEAK 38(17Q11.2) WILD-TYPE   319
D38V6, multiclass
                                           clus
vv                                          AMP PEAK 38(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               38
                                           clus
vv                                          AMP PEAK 38(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                319
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                                cls
clus                               0   1
  AMP PEAK 38(17Q11.2) MUTATED     3  43
  AMP PEAK 38(17Q11.2) WILD-TYPE  10 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(17Q11.2) MUTATED      3   43
  AMP PEAK 38(17Q11.2) WILD-TYPE   10  307
                        clus
vv                       AMP PEAK 38(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK 38(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            307
[1] 2 2
[1] FALSE

Clustering(39) Variable = AMP PEAK 39(17Q12) MUTATION ANALYSIS
D39V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 39(17Q12) MUTATED    54  14
  AMP PEAK 39(17Q12) WILD-TYPE 389  46
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          68                          435 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          14                           46 
$`AMP PEAK 39(17Q12) MUTATED`
TCGA-A5-A0GR TCGA-A5-A1OH TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AJ-A3QS 
       36.82        36.33         1.18         0.49         0.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0LH 
        1.71         0.99         5.95        39.42        45.53        36.36 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CP 
       28.54        37.78        13.28        16.96        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IO 
       11.08         4.77        19.36        17.75         2.96        38.70 
TCGA-AX-A3FX TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A11I TCGA-B5-A1MY 
        0.13         0.13        80.38        23.01        75.72        11.87 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M2 TCGA-BG-A0M4 
       12.79         5.03        34.13        34.95        20.94        34.98 
TCGA-BG-A0M6 TCGA-BK-A26L TCGA-BS-A0U8 TCGA-D1-A0ZP TCGA-D1-A16G TCGA-D1-A16I 
        7.92        24.13        97.41        29.95        27.42        11.51 
TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A2G0 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       18.67        18.25         3.52        35.38        12.39        91.96 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR 
       48.36        24.33        26.96         4.54        19.27        17.62 
TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       15.09         3.62        13.45        27.35        13.84         6.44 
TCGA-EY-A54A TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
        3.72         9.07        28.93        25.02        26.01        45.01 
TCGA-KJ-A3U4 TCGA-PG-A915 
        2.43         7.00 

$`AMP PEAK 39(17Q12) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       65.75        60.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
        1.94        15.95         1.87         2.33         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D 
       83.67        21.99        23.31        86.07         8.22        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89         7.86        12.20        20.91        48.79       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        97.71        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        18.25        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        65.88        19.20        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       40.50        26.33        27.32        31.13         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.33         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        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       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        33.11        41.06        18.61        20.19        19.33 
TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
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        23.47        85.55        78.21         4.80        77.95 
TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UA 
       61.87        67.99        96.49        30.74        67.20        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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         1.41 
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 
        6.77         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-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        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        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.01         7.36        16.80        10.92        18.81        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       27.16        22.26        16.34         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        18.84        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       15.81         8.55         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 
       18.87        22.82        45.76        31.04        29.10        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC 
       59.01        28.96        41.06         1.74        13.15        10.82 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                        0.13                         0.03 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                       97.41                       191.84 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                       18.46                        23.34 
[1] "0.1 - 97.4 (18.5)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "2.5"
D39V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 39(17Q12) MUTATED                                        18
  AMP PEAK 39(17Q12) WILD-TYPE                                     362
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 39(17Q12) MUTATED                               3
  AMP PEAK 39(17Q12) WILD-TYPE                            18
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 39(17Q12) MUTATED                                  48
  AMP PEAK 39(17Q12) WILD-TYPE                                56
D39V3, multiclass
                                         clus
vv                                        AMP PEAK 39(17Q12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         18
  MIXED SEROUS AND ENDOMETRIOID                                    3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               48
                                         clus
vv                                        AMP PEAK 39(17Q12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          362
  MIXED SEROUS AND ENDOMETRIOID                                     18
  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"
D39V4, binary
                              cls
clus                             0   1
  AMP PEAK 39(17Q12) MUTATED    19  50
  AMP PEAK 39(17Q12) WILD-TYPE 119 317
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 39(17Q12) MUTATED     19   50
  AMP PEAK 39(17Q12) WILD-TYPE  119  317
     clus
vv    AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE
  NO                          19                          119
  YES                         50                          317
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 39(17Q12) MUTATED    42   5   4   5
  AMP PEAK 39(17Q12) WILD-TYPE 309  17  13  25
D39V5, multiclass
    clus
vv   AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE
  R0                         42                          309
  R1                          5                           17
  R2                          4                           13
  RX                          5                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 39(17Q12) MUTATED                                  1     0
  AMP PEAK 39(17Q12) WILD-TYPE                                3    19
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 39(17Q12) MUTATED                          22
  AMP PEAK 39(17Q12) WILD-TYPE                        68
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 39(17Q12) MUTATED                                           0    45
  AMP PEAK 39(17Q12) WILD-TYPE                                         9   312
D39V6, multiclass
                                           clus
vv                                          AMP PEAK 39(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              0
  BLACK OR AFRICAN AMERICAN                                         22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             45
                                           clus
vv                                          AMP PEAK 39(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                           68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            9
  WHITE                                                              312
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                              cls
clus                             0   1
  AMP PEAK 39(17Q12) MUTATED     2  52
  AMP PEAK 39(17Q12) WILD-TYPE  11 298
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 39(17Q12) MUTATED      2   52
  AMP PEAK 39(17Q12) WILD-TYPE   11  298
                        clus
vv                       AMP PEAK 39(17Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         52
                        clus
vv                       AMP PEAK 39(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          298
[1] 2 2
[1] FALSE

Clustering(40) Variable = AMP PEAK 40(17Q25.1) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 40(17Q25.1) MUTATED    75  18
  AMP PEAK 40(17Q25.1) WILD-TYPE 368  42
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                            93                            410 
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                            18                             42 
$`AMP PEAK 40(17Q25.1) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-AJ-A23M 
       65.75        36.82        17.59        36.33        28.64         1.18 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH 
        1.08         0.49         1.12        22.26         0.92         0.76 
TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D 
       16.87         0.99        21.99         5.95        39.42        57.80 
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        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CF 
        0.56        53.92        28.54        37.78        13.28        76.83 
TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2HK 
       25.12        11.08         4.77        19.36        17.75         2.96 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN 
        0.33         0.13        20.52         0.13         0.13        80.38 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MY 
       23.01        17.85         4.11        75.72       102.31        11.87 
TCGA-B5-A1N2 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A3PP 
       12.79        20.94        34.98         7.92        36.49         6.81 
TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ 
       10.22        16.64        61.87        67.20        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         3.52 
TCGA-D1-A2G7 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
       44.88        35.38         9.37        91.96        48.36        24.33 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO 
       34.39        22.26        16.34        23.90         6.90        19.27 
TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       15.09        12.59        13.45        29.10        27.35         6.44 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
        3.72        34.98        96.69        26.01        45.01         1.74 
TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A915 
       13.15        23.97         7.00 

$`AMP PEAK 40(17Q25.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       91.04        46.32         5.33         5.16         7.33        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
        1.28        36.99        20.65         1.35        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
       15.95         1.87         1.71         2.33         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N 
       83.67        23.31        86.07         8.22        45.53         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
        6.71        30.90        10.42        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        35.01        43.82        40.11        65.88 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A2H4 
       20.05        72.56        54.12        67.50        36.39        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        27.32        31.13        38.70         0.23         0.10 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.03         0.23         1.18         8.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        33.11         5.03        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M9 
       18.61        20.19        19.33        35.21        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        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         6.21        10.16 
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        23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-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         1.41         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         6.77         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 
       18.02        15.06         1.05         3.95        41.42         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26         4.27         4.11        27.16        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        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       18.81        37.71        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        24.79        32.38        19.40        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       12.89        27.16        26.96         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
        8.15        24.36        27.16        23.34        23.34        22.78 
TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97        18.84        17.88        17.62        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 
       15.81         8.55         6.48        19.33         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A547 
       18.87        22.82        45.76        31.04        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
        2.14         6.97         5.29         5.88        40.01        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       36.00         7.99        13.84         8.98        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KJ-A3U4 TCGA-PG-A5BC 
       28.93        28.96        25.02        41.06         2.43        10.82 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        9.11        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                        125.42                         191.84 
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                        19.360                         23.425 
[1] "0.1 - 125.4 (19.4)" "0.0 - 191.8 (23.4)"
[1] "hr=" "2.2"
D40V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 40(17Q25.1) MUTATED                                        34
  AMP PEAK 40(17Q25.1) WILD-TYPE                                     346
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 40(17Q25.1) MUTATED                               9
  AMP PEAK 40(17Q25.1) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 40(17Q25.1) MUTATED                                  51
  AMP PEAK 40(17Q25.1) WILD-TYPE                                53
D40V3, multiclass
                                         clus
vv                                        AMP PEAK 40(17Q25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           34
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 51
                                         clus
vv                                        AMP PEAK 40(17Q25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            346
  MIXED SEROUS AND ENDOMETRIOID                                       12
  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"
D40V4, binary
                                cls
clus                               0   1
  AMP PEAK 40(17Q25.1) MUTATED    23  71
  AMP PEAK 40(17Q25.1) WILD-TYPE 115 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(17Q25.1) MUTATED     23   71
  AMP PEAK 40(17Q25.1) WILD-TYPE  115  296
     clus
vv    AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE
  NO                            23                            115
  YES                           71                            296
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 40(17Q25.1) MUTATED    60   4   5   9
  AMP PEAK 40(17Q25.1) WILD-TYPE 291  18  12  21
D40V5, multiclass
    clus
vv   AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE
  R0                           60                            291
  R1                            4                             18
  R2                            5                             12
  RX                            9                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 40(17Q25.1) MUTATED                                  0     0
  AMP PEAK 40(17Q25.1) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 40(17Q25.1) MUTATED                          32
  AMP PEAK 40(17Q25.1) WILD-TYPE                        58
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 40(17Q25.1) MUTATED                                           2
  AMP PEAK 40(17Q25.1) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 40(17Q25.1) MUTATED      56
  AMP PEAK 40(17Q25.1) WILD-TYPE   301
D40V6, multiclass
                                           clus
vv                                          AMP PEAK 40(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               56
                                           clus
vv                                          AMP PEAK 40(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                301
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                                cls
clus                               0   1
  AMP PEAK 40(17Q25.1) MUTATED     1  69
  AMP PEAK 40(17Q25.1) WILD-TYPE  12 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(17Q25.1) MUTATED      1   69
  AMP PEAK 40(17Q25.1) WILD-TYPE   12  281
                        clus
vv                       AMP PEAK 40(17Q25.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       AMP PEAK 40(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            281
[1] 2 2
[1] FALSE

Clustering(41) Variable = AMP PEAK 41(18P11.31) MUTATION ANALYSIS
D41V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 41(18P11.31) MUTATED    74  15
  AMP PEAK 41(18P11.31) WILD-TYPE 369  45
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             89                             414 
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             15                              45 
$`AMP PEAK 41(18P11.31) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       37.02       105.37        36.82        19.96        11.44        36.33 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF 
       14.96         1.08         0.49        22.26         0.92         1.35 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05A TCGA-AP-A0L8 
        0.76        16.87         1.71         0.99        39.42        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A3K1 
      125.42         3.39        97.71        33.40        41.95        18.25 
TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       33.73        37.78        15.25        20.28        12.43        76.83 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HK 
        4.77        30.12        71.24        61.18        33.40         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0K8 
       38.70         0.33         0.13         0.03         0.13        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
        4.11        75.72         5.03        34.13        34.95         7.92 
TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 
       36.49        24.39        23.70        10.22        24.13        67.20 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A2G0 TCGA-D1-A2G7 
       39.48        37.32        18.67         0.72         3.52        44.88 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
        4.11        35.38         9.37        91.96        48.36        24.33 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A210 
       32.38        19.40        27.16        22.26        17.62        12.59 
TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY 
        3.62        13.45        29.10        17.92         5.88        34.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       59.01         9.07        28.93        25.02        26.01        45.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       13.15         2.43        10.82        23.97         7.00 

$`AMP PEAK 41(18P11.31) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95         7.92         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O 
       28.64         5.33         5.16         7.33         1.18         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        1.28        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        1.87         2.33         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H 
        5.95        23.31        86.07         8.22        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S 
       30.90        10.42        27.85        16.24         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       11.08        33.53        68.71        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       17.75        27.32        31.13         0.23         0.10         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.13         0.23         1.18         8.35        14.47 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        17.88        13.74        17.10        11.01         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY 
      102.31        50.89        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       33.11        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        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       21.17        20.28        15.42        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 
       14.73        14.01        15.45        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
        9.57        35.67        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         6.21        10.16        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        23.47        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        88.34        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        62.79        63.58        49.55 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         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         6.77         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-A2G5 
       18.02         2.07        15.06         1.05         3.95        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48         0.26         4.27        27.16        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        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       18.81        37.71        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        24.79        34.39        19.36        35.15        12.89 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       26.96        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       13.97         6.90        19.27        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       14.40        18.87        22.82        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84         6.44         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A6IB TCGA-PG-A914 
       96.69        28.96        41.06         1.74         9.11        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                         125.42                          191.84 
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                         22.260                          22.965 
[1] "0.0 - 125.4 (22.3)" "0.1 - 191.8 (23.0)"
[1] "hr=" "1.7"
D41V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 41(18P11.31) MUTATED                                        27
  AMP PEAK 41(18P11.31) WILD-TYPE                                     353
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 41(18P11.31) MUTATED                               6
  AMP PEAK 41(18P11.31) WILD-TYPE                            15
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 41(18P11.31) MUTATED                                  56
  AMP PEAK 41(18P11.31) WILD-TYPE                                48
D41V3, multiclass
                                         clus
vv                                        AMP PEAK 41(18P11.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            27
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  56
                                         clus
vv                                        AMP PEAK 41(18P11.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             353
  MIXED SEROUS AND ENDOMETRIOID                                        15
  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"
D41V4, binary
                                 cls
clus                                0   1
  AMP PEAK 41(18P11.31) MUTATED    15  74
  AMP PEAK 41(18P11.31) WILD-TYPE 123 293
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 41(18P11.31) MUTATED     15   74
  AMP PEAK 41(18P11.31) WILD-TYPE  123  293
     clus
vv    AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE
  NO                             15                             123
  YES                            74                             293
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 41(18P11.31) MUTATED    58   3   8   7
  AMP PEAK 41(18P11.31) WILD-TYPE 293  19   9  23
D41V5, multiclass
    clus
vv   AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE
  R0                            58                             293
  R1                             3                              19
  R2                             8                               9
  RX                             7                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 41(18P11.31) MUTATED                                  0     3
  AMP PEAK 41(18P11.31) WILD-TYPE                                4    16
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 41(18P11.31) MUTATED                          30
  AMP PEAK 41(18P11.31) WILD-TYPE                        60
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 41(18P11.31) MUTATED                                           1
  AMP PEAK 41(18P11.31) WILD-TYPE                                         8
                                 vv
clus                              WHITE
  AMP PEAK 41(18P11.31) MUTATED      51
  AMP PEAK 41(18P11.31) WILD-TYPE   306
D41V6, multiclass
                                           clus
vv                                          AMP PEAK 41(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                            30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                51
                                           clus
vv                                          AMP PEAK 41(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  16
  BLACK OR AFRICAN AMERICAN                                              60
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               8
  WHITE                                                                 306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                                 cls
clus                                0   1
  AMP PEAK 41(18P11.31) MUTATED     2  63
  AMP PEAK 41(18P11.31) WILD-TYPE  11 287
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 41(18P11.31) MUTATED      2   63
  AMP PEAK 41(18P11.31) WILD-TYPE   11  287
                        clus
vv                       AMP PEAK 41(18P11.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            63
                        clus
vv                       AMP PEAK 41(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             287
[1] 2 2
[1] FALSE

Clustering(42) Variable = AMP PEAK 42(18Q11.2) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 42(18Q11.2) MUTATED    51  13
  AMP PEAK 42(18Q11.2) WILD-TYPE 392  47
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            64                            439 
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            13                             47 
$`AMP PEAK 42(18Q11.2) MUTATED`
TCGA-A5-A0GE TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3EM 
      105.37        19.96        36.33         1.08         0.85        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05J 
        0.92         1.35         0.76        16.87         1.71        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A3K1 
       48.79       125.42         3.39        33.40        41.95        18.25 
TCGA-AP-A5FX TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A3G3 
       33.73        30.12        71.24        61.18        33.40         0.03 
TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD 
       80.38        75.72        11.87        12.79         5.03        34.13 
TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC 
       34.95        36.49        24.39        23.70         6.81        10.22 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S 
       24.13        67.20        22.55        39.48        11.51        18.67 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
        3.52        44.88         4.11        35.38         9.37        91.96 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EY-A1GR TCGA-EY-A210 
       48.36        24.33        34.39        26.96        17.62        12.59 
TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A72D 
        3.62        13.45        29.10        27.35         6.44         5.88 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-PG-A915 
       59.01        28.93        26.01         7.00 

$`AMP PEAK 42(18Q11.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78         3.22        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        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         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.18         1.97         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40         3.02         0.49         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68         1.64        14.66        22.49         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW 
       20.65        15.62         1.94        15.95         1.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
        7.86        12.20        20.91       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        31.30        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S 
       30.90        10.42        27.85        16.24         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
        4.77        33.53        68.71        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.10         0.33         0.13         0.20        20.52         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.23         1.18         8.35        14.47         0.13        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      102.31        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        33.11        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       35.67        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        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 
        1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
       15.06         1.05         3.95        41.42         8.48         0.26 
TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.01         7.36        16.80        10.92        18.81        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       32.38        19.40        19.36        35.15        12.89        27.16 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       22.26        16.34         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       13.97         6.90        19.27        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       14.40        18.87        22.82        45.76        31.04        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       17.92         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       34.98        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       96.69         9.07        28.96        25.02        41.06        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        1.74        13.15         2.43        10.82         9.11        23.97 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       12.92        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                        125.42                         191.84 
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                         24.23                          22.49 
[1] "0.0 - 125.4 (24.2)" "0.1 - 191.8 (22.5)"
[1] "hr=" "1.9"
D42V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 42(18Q11.2) MUTATED                                        18
  AMP PEAK 42(18Q11.2) WILD-TYPE                                     362
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 42(18Q11.2) MUTATED                               4
  AMP PEAK 42(18Q11.2) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 42(18Q11.2) MUTATED                                  42
  AMP PEAK 42(18Q11.2) WILD-TYPE                                62
D42V3, multiclass
                                         clus
vv                                        AMP PEAK 42(18Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           18
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 42
                                         clus
vv                                        AMP PEAK 42(18Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            362
  MIXED SEROUS AND ENDOMETRIOID                                       17
  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"
D42V4, binary
                                cls
clus                               0   1
  AMP PEAK 42(18Q11.2) MUTATED    14  50
  AMP PEAK 42(18Q11.2) WILD-TYPE 124 317
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(18Q11.2) MUTATED     14   50
  AMP PEAK 42(18Q11.2) WILD-TYPE  124  317
     clus
vv    AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE
  NO                            14                            124
  YES                           50                            317
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 42(18Q11.2) MUTATED    40   1   4   8
  AMP PEAK 42(18Q11.2) WILD-TYPE 311  21  13  22
D42V5, multiclass
    clus
vv   AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE
  R0                           40                            311
  R1                            1                             21
  R2                            4                             13
  RX                            8                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 42(18Q11.2) MUTATED                                  0     1
  AMP PEAK 42(18Q11.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 42(18Q11.2) MUTATED                          23
  AMP PEAK 42(18Q11.2) WILD-TYPE                        67
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 42(18Q11.2) MUTATED                                           1
  AMP PEAK 42(18Q11.2) WILD-TYPE                                         8
                                vv
clus                             WHITE
  AMP PEAK 42(18Q11.2) MUTATED      36
  AMP PEAK 42(18Q11.2) WILD-TYPE   321
D42V6, multiclass
                                           clus
vv                                          AMP PEAK 42(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               36
                                           clus
vv                                          AMP PEAK 42(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                                cls
clus                               0   1
  AMP PEAK 42(18Q11.2) MUTATED     1  43
  AMP PEAK 42(18Q11.2) WILD-TYPE  12 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(18Q11.2) MUTATED      1   43
  AMP PEAK 42(18Q11.2) WILD-TYPE   12  307
                        clus
vv                       AMP PEAK 42(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK 42(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            307
[1] 2 2
[1] FALSE

Clustering(43) Variable = AMP PEAK 43(19P13.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 43(19P13.2) MUTATED    72  17
  AMP PEAK 43(19P13.2) WILD-TYPE 371  43
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            89                            414 
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            17                             43 
$`AMP PEAK 43(19P13.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QM 
       37.02        65.75        36.33        14.96         1.08         0.85 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
        2.24         1.64        22.26         1.35        16.87         1.71 
TCGA-AJ-A8CW TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        0.13         5.95        39.42        45.53        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW 
        3.39        97.71        41.95        33.73        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       16.96        13.55        36.39        11.08         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2IO TCGA-AX-A3G1 TCGA-AX-A3G4 
       33.53        61.18        19.36        38.70        20.52         0.13 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I 
        0.23         0.13        80.38        23.01        17.85        75.72 
TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0VT TCGA-BG-A0YV 
      102.31        12.79         5.03        34.95        24.39        12.56 
TCGA-BK-A0CC TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16S 
       10.22        49.55        29.95        22.55        11.51        18.67 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 
        6.77        28.08        13.22         0.72        18.25         2.07 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A8L9 
       44.88         4.11        35.38        31.10        91.96        24.33 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU 
       10.92        37.71        24.79        19.40        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2ON 
       16.34        23.90        17.62        12.59         3.62        13.45 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2F8 
       29.10        27.35         6.44        17.92        34.98        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.01        45.01        23.97        12.92         7.00 

$`AMP PEAK 43(19P13.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        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         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        7.33         1.18         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        3.02         0.49         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49         1.28         0.92        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU 
        0.76         1.94        15.95         1.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.70        83.67        21.99        23.31        86.07         8.22 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       57.80        36.89         7.86        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       18.25         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.01        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       15.25        20.28        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A2HC 
       54.12        67.50        25.12        30.12        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       40.50        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 
        0.23         0.10         0.33         0.13         0.20         0.03 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
        4.11         8.71       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 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       33.11        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       11.31         6.81        35.90        34.98         6.21        10.16 
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        23.47        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 
       67.20        88.34        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        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        19.79         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30         9.37        12.39        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37         6.67        16.01         7.36        16.80        18.81 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       31.96        35.05        33.01        27.12        57.60        32.38 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G7 
       34.39        19.36        35.15        12.89        27.16         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
        6.48        19.33        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       31.04        13.84         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       41.06         1.74        13.15         2.43        10.82         9.11 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                        125.42                         191.84 
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                         22.26                          23.26 
[1] "0.1 - 125.4 (22.3)" "0.0 - 191.8 (23.3)"
[1] "hr=" "2"  
D43V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 43(19P13.2) MUTATED                                        23
  AMP PEAK 43(19P13.2) WILD-TYPE                                     357
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 43(19P13.2) MUTATED                               7
  AMP PEAK 43(19P13.2) WILD-TYPE                            14
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 43(19P13.2) MUTATED                                  60
  AMP PEAK 43(19P13.2) WILD-TYPE                                44
D43V3, multiclass
                                         clus
vv                                        AMP PEAK 43(19P13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           23
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 60
                                         clus
vv                                        AMP PEAK 43(19P13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            357
  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"
D43V4, binary
                                cls
clus                               0   1
  AMP PEAK 43(19P13.2) MUTATED    17  73
  AMP PEAK 43(19P13.2) WILD-TYPE 121 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 43(19P13.2) MUTATED     17   73
  AMP PEAK 43(19P13.2) WILD-TYPE  121  294
     clus
vv    AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE
  NO                            17                            121
  YES                           73                            294
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 43(19P13.2) MUTATED    59   6   5   7
  AMP PEAK 43(19P13.2) WILD-TYPE 292  16  12  23
D43V5, multiclass
    clus
vv   AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE
  R0                           59                            292
  R1                            6                             16
  R2                            5                             12
  RX                            7                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 43(19P13.2) MUTATED                                  0     0
  AMP PEAK 43(19P13.2) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 43(19P13.2) MUTATED                          28
  AMP PEAK 43(19P13.2) WILD-TYPE                        62
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 43(19P13.2) MUTATED                                           2
  AMP PEAK 43(19P13.2) WILD-TYPE                                         7
                                vv
clus                             WHITE
  AMP PEAK 43(19P13.2) MUTATED      53
  AMP PEAK 43(19P13.2) WILD-TYPE   304
D43V6, multiclass
                                           clus
vv                                          AMP PEAK 43(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               53
                                           clus
vv                                          AMP PEAK 43(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             62
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                304
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                                cls
clus                               0   1
  AMP PEAK 43(19P13.2) MUTATED     2  62
  AMP PEAK 43(19P13.2) WILD-TYPE  11 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 43(19P13.2) MUTATED      2   62
  AMP PEAK 43(19P13.2) WILD-TYPE   11  288
                        clus
vv                       AMP PEAK 43(19P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK 43(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            288
[1] 2 2
[1] FALSE

Clustering(44) Variable = AMP PEAK 44(19Q12) MUTATION ANALYSIS
D44V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 44(19Q12) MUTATED    84  22
  AMP PEAK 44(19Q12) WILD-TYPE 359  38
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                         106                          397 
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                          22                           38 
$`AMP PEAK 44(19Q12) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A3LP 
       37.02        11.44        36.33        91.04        46.32        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        1.18         1.08         0.49         1.12         2.24         1.64 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW 
        0.92         0.76        16.87         1.71         0.99         0.13 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       21.99        39.42        57.80        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        41.95        33.73        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       16.96        13.55        20.28        11.08         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G3 
       33.53        61.18        19.36         2.96        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.13         0.23         0.13        80.38        17.85         4.11 
TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       75.72        11.87        12.79         5.03        34.13        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
        7.92        36.49        24.39         6.81        10.22        24.13 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G 
       16.64        67.20        49.55        22.55        39.48        27.42 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-DI-A1NO 
       11.51        18.67         0.72        18.25         2.07         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A22Y 
       12.39        31.10        91.96        48.36        10.92        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GR 
       32.38        19.40        22.26        16.34         6.90        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 
       15.09        15.81        12.59        29.10         6.44        17.92 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX 
        3.72         5.88        40.01        34.98        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       28.93        25.02        26.01        41.06        45.01        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
        2.43        10.82        23.97         7.00 

$`AMP PEAK 44(19Q12) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O 
        8.02        28.64         5.33         5.16         7.33         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79         0.85         2.40         3.02         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68        14.66        22.49        22.26         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.33         2.70        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
        8.22        36.89         7.86        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37         3.39        63.16        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       18.25         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.01        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HA TCGA-AX-A2HC 
       67.50        25.12        36.39        30.12        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       40.50        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G8 
        0.23         0.10         0.33         0.13         0.20         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        23.01        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       15.29       116.25        96.30        78.81        62.14        33.11 
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 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        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 
        6.21        10.16        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        23.47        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 
       88.34        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        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93         1.74         4.44        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         1.41         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         6.77 
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-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
        8.48        44.88         0.26         4.27         4.11        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-E6-A1LX 
       16.31        39.29        36.62        24.30        35.38        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        24.33        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        18.81        37.71        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       27.12        57.60        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       27.16        26.96         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97        19.27        18.84        17.88        16.11        12.43 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        8.55         6.48        19.33         3.62        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        13.45        45.76        31.04        27.35        13.84 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        2.14         6.97         5.29        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-PG-A6IB 
       13.84         8.98        96.69        28.96         1.74         9.11 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       12.92        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                        0.03                         0.10 
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                      125.42                       191.84 
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                      18.085                       23.470 
[1] "0.0 - 125.4 (18.1)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.6"
D44V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 44(19Q12) MUTATED                                        25
  AMP PEAK 44(19Q12) WILD-TYPE                                     355
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 44(19Q12) MUTATED                              10
  AMP PEAK 44(19Q12) WILD-TYPE                            11
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 44(19Q12) MUTATED                                  71
  AMP PEAK 44(19Q12) WILD-TYPE                                33
D44V3, multiclass
                                         clus
vv                                        AMP PEAK 44(19Q12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         25
  MIXED SEROUS AND ENDOMETRIOID                                   10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               71
                                         clus
vv                                        AMP PEAK 44(19Q12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          355
  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"
D44V4, binary
                              cls
clus                             0   1
  AMP PEAK 44(19Q12) MUTATED    25  81
  AMP PEAK 44(19Q12) WILD-TYPE 113 286
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(19Q12) MUTATED     25   81
  AMP PEAK 44(19Q12) WILD-TYPE  113  286
     clus
vv    AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE
  NO                          25                          113
  YES                         81                          286
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 44(19Q12) MUTATED    69   5   6   9
  AMP PEAK 44(19Q12) WILD-TYPE 282  17  11  21
D44V5, multiclass
    clus
vv   AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE
  R0                         69                          282
  R1                          5                           17
  R2                          6                           11
  RX                          9                           21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 44(19Q12) MUTATED                                  1     2
  AMP PEAK 44(19Q12) WILD-TYPE                                3    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 44(19Q12) MUTATED                          38
  AMP PEAK 44(19Q12) WILD-TYPE                        52
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 44(19Q12) MUTATED                                           3    57
  AMP PEAK 44(19Q12) WILD-TYPE                                         6   300
D44V6, multiclass
                                           clus
vv                                          AMP PEAK 44(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         38
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          3
  WHITE                                                             57
                                           clus
vv                                          AMP PEAK 44(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            6
  WHITE                                                              300
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                              cls
clus                             0   1
  AMP PEAK 44(19Q12) MUTATED     3  72
  AMP PEAK 44(19Q12) WILD-TYPE  10 278
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(19Q12) MUTATED      3   72
  AMP PEAK 44(19Q12) WILD-TYPE   10  278
                        clus
vv                       AMP PEAK 44(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         72
                        clus
vv                       AMP PEAK 44(19Q12) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          278
[1] 2 2
[1] FALSE

Clustering(45) Variable = AMP PEAK 45(20P13) MUTATION ANALYSIS
D45V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 45(20P13) MUTATED    95  14
  AMP PEAK 45(20P13) WILD-TYPE 348  46
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                         109                          394 
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                          14                           46 
$`AMP PEAK 45(20P13) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 
       37.02        65.75        11.44        36.33        91.04        46.32 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QN TCGA-AJ-A3BI 
        7.33        14.96         1.18         1.08         2.40         2.24 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A05D 
        1.64        22.26         0.92         0.76         1.71        57.80 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AX-A0IU 
      125.42         3.39        55.89        31.30        41.95        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 
       37.78        16.96        20.28        12.43        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 
       30.12         2.96        38.70         0.13         0.20         0.23 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L 
        0.13        80.38        43.13         4.11        75.72        45.90 
TCGA-B5-A11V TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
       19.56        11.87        12.79       116.25        33.11         5.03 
TCGA-B5-A5OD TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A18C 
       34.13        30.81        24.39        52.83        12.56        15.45 
TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
        1.81        10.22        10.16        24.13        16.64        13.18 
TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZU TCGA-D1-A0ZZ 
        4.80        67.20        72.72        49.55        28.67        22.55 
TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S 
        4.44        37.32        11.51        29.92        31.07        18.67 
TCGA-D1-A1NW TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-E6-A8L9 
        0.72        41.42         4.11         9.37        48.36        24.33 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       10.92        37.71        24.79        32.38        19.40        34.39 
TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GJ 
       35.15        26.96        22.26         6.21         4.54        23.90 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OQ 
        6.90        17.62        15.09         3.62        14.40        29.10 
TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       27.35         3.72        40.01        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       25.02        26.01        45.01        13.15        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 45(20P13) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       28.64         5.33         5.16         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        0.85         3.02         0.49         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87        16.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        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 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       25.08        71.67        60.36        35.54        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       25.12        36.39        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G3 
       31.13         0.23         0.10         0.33        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.13         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         8.71       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        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       27.35        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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE 
       15.29        96.30        78.81        62.14        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        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        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        15.42        26.66        16.34        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-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
        6.81        35.90        34.98         6.21        31.76        24.99 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        23.47        85.55        78.21 
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-A0UV TCGA-BS-A0V4 
       88.34        85.84        82.39        81.57        73.25        59.51 
TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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 
        1.41         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         6.77         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         3.52         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 
       35.38        12.39        31.10        91.96        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37         6.67        16.01         7.36        16.80        18.81 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU 
       31.96        35.05        33.01        27.12        57.60        19.36 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       12.89        27.16        16.34        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO 
       27.16        23.34        23.34        22.78        13.97        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       18.84        17.88        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33        12.59        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        13.84         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         5.29         5.88        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A3PV 
        7.99        13.84         8.98        96.69        28.96        41.06 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        1.74         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                        0.13                         0.03 
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                      125.42                       191.84 
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                       20.28                        23.26 
[1] "0.1 - 125.4 (20.3)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.3"
D45V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 45(20P13) MUTATED                                        50
  AMP PEAK 45(20P13) WILD-TYPE                                     330
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 45(20P13) MUTATED                               5
  AMP PEAK 45(20P13) WILD-TYPE                            16
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 45(20P13) MUTATED                                  55
  AMP PEAK 45(20P13) WILD-TYPE                                49
D45V3, multiclass
                                         clus
vv                                        AMP PEAK 45(20P13) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         50
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               55
                                         clus
vv                                        AMP PEAK 45(20P13) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          330
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                              cls
clus                             0   1
  AMP PEAK 45(20P13) MUTATED    21  89
  AMP PEAK 45(20P13) WILD-TYPE 117 278
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 45(20P13) MUTATED     21   89
  AMP PEAK 45(20P13) WILD-TYPE  117  278
     clus
vv    AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE
  NO                          21                          117
  YES                         89                          278
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 45(20P13) MUTATED    73   4   6   6
  AMP PEAK 45(20P13) WILD-TYPE 278  18  11  24
D45V5, multiclass
    clus
vv   AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE
  R0                         73                          278
  R1                          4                           18
  R2                          6                           11
  RX                          6                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 45(20P13) MUTATED                                  0     4
  AMP PEAK 45(20P13) WILD-TYPE                                4    15
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 45(20P13) MUTATED                          30
  AMP PEAK 45(20P13) WILD-TYPE                        60
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 45(20P13) MUTATED                                           2    66
  AMP PEAK 45(20P13) WILD-TYPE                                         7   291
D45V6, multiclass
                                           clus
vv                                          AMP PEAK 45(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              4
  BLACK OR AFRICAN AMERICAN                                         30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             66
                                           clus
vv                                          AMP PEAK 45(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               15
  BLACK OR AFRICAN AMERICAN                                           60
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  WHITE                                                              291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                              cls
clus                             0   1
  AMP PEAK 45(20P13) MUTATED     1  74
  AMP PEAK 45(20P13) WILD-TYPE  12 276
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 45(20P13) MUTATED      1   74
  AMP PEAK 45(20P13) WILD-TYPE   12  276
                        clus
vv                       AMP PEAK 45(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         74
                        clus
vv                       AMP PEAK 45(20P13) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          276
[1] 2 2
[1] FALSE

Clustering(46) Variable = AMP PEAK 46(20Q11.21) MUTATION ANALYSIS
D46V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 46(20Q11.21) MUTATED   114  25
  AMP PEAK 46(20Q11.21) WILD-TYPE 329  35
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                            139                             364 
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                             25                              35 
$`AMP PEAK 46(20Q11.21) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 
      149.56        37.02        11.44        36.33        46.32        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN 
        7.33        14.96         1.18         1.08         0.39         2.40 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        0.49         2.24         1.64        22.26         1.28         0.92 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
        0.76        16.87         1.71        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DO 
       36.89        48.79       125.42         3.39        97.71        31.30 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       41.95        18.25        53.92        28.54        37.78        16.96 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HF 
       20.28        12.43        11.08         4.77        30.12        19.36 
TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        2.96         0.23         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT 
        0.03         0.13         0.23         0.13        80.38        43.13 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V 
       23.01        17.85         4.11        75.72        45.90        19.56 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
      102.31        11.87        12.79       116.25        33.11         5.03 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       34.13        34.95         7.92        36.49        30.81        24.39 
TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       52.83        15.45         1.81        10.22        10.16        24.13 
TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZQ 
       13.18         4.80        67.20        72.72        49.55         8.55 
TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S 
        4.44        37.32        11.51        29.92        31.07        18.67 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH 
        6.77        28.08         0.72         2.07        41.42         4.11 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 
       35.38        12.39        91.96        48.36        24.33        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV 
       18.81        37.71        24.79        32.38        19.40        35.15 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GJ TCGA-EY-A1GM 
       26.96        22.26        16.34         6.21        23.90         6.90 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A214 
       17.62        15.09         8.55         6.48        12.59        14.40 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A54A 
       13.45        29.10        27.35        13.84        17.92         3.72 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        5.88        40.01        36.00        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       25.02        41.06        45.01        13.15        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 46(20Q11.21) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM 
       91.04         5.33         5.16         1.97        19.79         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        3.02         1.12         0.76         1.68        14.66        22.49 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.87         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       21.99         5.95        23.31        86.07         8.22         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20        20.91       117.99       110.37        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        35.01        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       19.20        13.55        15.25        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        68.71        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 
       27.32        31.13        38.70         0.10         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q 
       88.34        54.44        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       33.50        27.35        16.73        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       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW 
       15.29        96.30        78.81        62.14        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        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        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        39.32        21.17        20.28        15.42        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       16.34        34.29        52.64        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 
       13.78        14.73        14.01        15.45        14.27         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 
       34.98         6.21        31.76        24.99        16.64        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        23.47        85.55        78.21        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        88.34 
TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        73.25        59.51        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-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 
        1.41         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-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         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48        44.88         0.26         4.27        27.16        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 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS 
       31.96        35.05        33.01        27.12        57.60        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       19.36        12.89        27.16        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33         3.62        18.87        22.82        45.76        31.04 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 
        6.44         2.14         6.97         5.29        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F9 
        7.99        13.84         8.98        96.69        28.96        26.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        1.74         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                         149.56                          191.84 
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                         18.670                          23.585 
[1] "0.0 - 149.6 (18.7)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.2"
D46V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 46(20Q11.21) MUTATED                                        58
  AMP PEAK 46(20Q11.21) WILD-TYPE                                     322
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 46(20Q11.21) MUTATED                               6
  AMP PEAK 46(20Q11.21) WILD-TYPE                            15
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 46(20Q11.21) MUTATED                                  76
  AMP PEAK 46(20Q11.21) WILD-TYPE                                28
D46V3, multiclass
                                         clus
vv                                        AMP PEAK 46(20Q11.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            58
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  76
                                         clus
vv                                        AMP PEAK 46(20Q11.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             322
  MIXED SEROUS AND ENDOMETRIOID                                        15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                                 cls
clus                                0   1
  AMP PEAK 46(20Q11.21) MUTATED    27 113
  AMP PEAK 46(20Q11.21) WILD-TYPE 111 254
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 46(20Q11.21) MUTATED     27  113
  AMP PEAK 46(20Q11.21) WILD-TYPE  111  254
     clus
vv    AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE
  NO                             27                             111
  YES                           113                             254
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 46(20Q11.21) MUTATED    90   5   9   8
  AMP PEAK 46(20Q11.21) WILD-TYPE 261  17   8  22
D46V5, multiclass
    clus
vv   AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE
  R0                            90                             261
  R1                             5                              17
  R2                             9                               8
  RX                             8                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 46(20Q11.21) MUTATED                                  1     5
  AMP PEAK 46(20Q11.21) WILD-TYPE                                3    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 46(20Q11.21) MUTATED                          38
  AMP PEAK 46(20Q11.21) WILD-TYPE                        52
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 46(20Q11.21) MUTATED                                           3
  AMP PEAK 46(20Q11.21) WILD-TYPE                                         6
                                 vv
clus                              WHITE
  AMP PEAK 46(20Q11.21) MUTATED      84
  AMP PEAK 46(20Q11.21) WILD-TYPE   273
D46V6, multiclass
                                           clus
vv                                          AMP PEAK 46(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            38
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                84
                                           clus
vv                                          AMP PEAK 46(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  WHITE                                                                 273
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                 cls
clus                                0   1
  AMP PEAK 46(20Q11.21) MUTATED     5  91
  AMP PEAK 46(20Q11.21) WILD-TYPE   8 259
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 46(20Q11.21) MUTATED      5   91
  AMP PEAK 46(20Q11.21) WILD-TYPE    8  259
                        clus
vv                       AMP PEAK 46(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            91
                        clus
vv                       AMP PEAK 46(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             259
[1] 2 2
[1] FALSE

Clustering(47) Variable = AMP PEAK 47(20Q13.12) MUTATION ANALYSIS
D47V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 47(20Q13.12) MUTATED   116  23
  AMP PEAK 47(20Q13.12) WILD-TYPE 327  37
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                            139                             364 
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                             23                              37 
$`AMP PEAK 47(20Q13.12) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 
      149.56        19.96        11.44        36.33        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN 
       28.64         7.33         1.18         1.08         0.39         2.40 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH 
        0.49         2.24         1.64        22.26         0.92         0.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A0L9 TCGA-AP-A0LF 
       16.87         1.71         5.95        39.42       125.42         3.39 
TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU 
       97.71        31.30        41.95        18.25        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR 
       37.78        16.96        13.55        20.28        12.43        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX 
        4.77        30.12        71.24         2.96         0.23         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.20        20.52         0.03         0.13         0.23         0.13 
TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L 
       80.38        43.13        17.85         4.11        75.72        45.90 
TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
       19.56       191.84       102.31        11.87        12.79       116.25 
TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0MS 
       78.81        33.11         5.03        34.95        36.49        30.81 
TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC 
       24.39        52.83        12.56        15.45         1.81        10.22 
TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 
       24.13        13.18         4.80        67.20        72.72        49.55 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J 
       29.95         8.55         4.44        37.32        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 TCGA-D1-A179 TCGA-D1-A17K 
       31.07        18.67         1.41        30.15         6.77        28.08 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN 
        0.72        18.25         2.07        41.42         4.11        35.38 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       12.39        91.96        48.36        24.33        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 
       37.71        24.79        32.38        19.40        35.15        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR 
       22.26        16.34         6.21        23.90         6.90        17.62 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2ON 
       15.09         8.55         6.48        12.59        14.40        13.45 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D 
       29.10        27.35         6.44        17.92         3.72         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 
       40.01        34.98        36.00        59.01         9.07        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       26.01        41.06        45.01        13.15        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`AMP PEAK 47(20Q13.12) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        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-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.33         5.16        14.96         1.97        19.79         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        3.02         1.12         0.76         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
        1.28        36.99        20.65         1.35        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       15.95         1.87         2.33         0.99         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D 
       83.67        21.99        23.31        86.07         8.22        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.10         0.33         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       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        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       27.35        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        14.40        14.70        11.70        15.29        96.30 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
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 
       39.32        21.17        20.28        15.42        26.66        16.34 
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-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        14.27         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.16        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        23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZR TCGA-D1-A0ZS 
       63.16        66.48        16.83        19.79         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-A16X TCGA-D1-A16Y 
       27.42        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       19.53         6.64        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-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       13.22        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-A2KZ 
        3.52         8.48        44.88         0.26         4.27        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30         9.37        31.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EY-A1G8 TCGA-EY-A1GC 
       34.39        19.36        12.89        27.16        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
        8.15        24.36        27.16        23.34        23.34        22.78 
TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97        19.27        18.84        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       15.81        19.33         3.62        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2D0 
       31.04        13.84         2.14         6.97         5.29        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        28.93        28.96 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        1.74         2.43        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                         191.84                          185.79 
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                          18.67                           23.47 
[1] "0.0 - 191.8 (18.7)" "0.1 - 185.8 (23.5)"
[1] "hr=" "1.9"
D47V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 47(20Q13.12) MUTATED                                        60
  AMP PEAK 47(20Q13.12) WILD-TYPE                                     320
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 47(20Q13.12) MUTATED                               7
  AMP PEAK 47(20Q13.12) WILD-TYPE                            14
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 47(20Q13.12) MUTATED                                  73
  AMP PEAK 47(20Q13.12) WILD-TYPE                                31
D47V3, multiclass
                                         clus
vv                                        AMP PEAK 47(20Q13.12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            60
  MIXED SEROUS AND ENDOMETRIOID                                       7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  73
                                         clus
vv                                        AMP PEAK 47(20Q13.12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             320
  MIXED SEROUS AND ENDOMETRIOID                                        14
  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"
D47V4, binary
                                 cls
clus                                0   1
  AMP PEAK 47(20Q13.12) MUTATED    24 116
  AMP PEAK 47(20Q13.12) WILD-TYPE 114 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 47(20Q13.12) MUTATED     24  116
  AMP PEAK 47(20Q13.12) WILD-TYPE  114  251
     clus
vv    AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE
  NO                             24                             114
  YES                           116                             251
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 47(20Q13.12) MUTATED    87   7   9  10
  AMP PEAK 47(20Q13.12) WILD-TYPE 264  15   8  20
D47V5, multiclass
    clus
vv   AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE
  R0                            87                             264
  R1                             7                              15
  R2                             9                               8
  RX                            10                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 47(20Q13.12) MUTATED                                  1     5
  AMP PEAK 47(20Q13.12) WILD-TYPE                                3    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 47(20Q13.12) MUTATED                          38
  AMP PEAK 47(20Q13.12) WILD-TYPE                        52
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 47(20Q13.12) MUTATED                                           3
  AMP PEAK 47(20Q13.12) WILD-TYPE                                         6
                                 vv
clus                              WHITE
  AMP PEAK 47(20Q13.12) MUTATED      83
  AMP PEAK 47(20Q13.12) WILD-TYPE   274
D47V6, multiclass
                                           clus
vv                                          AMP PEAK 47(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            38
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                83
                                           clus
vv                                          AMP PEAK 47(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  WHITE                                                                 274
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                 cls
clus                                0   1
  AMP PEAK 47(20Q13.12) MUTATED     5  95
  AMP PEAK 47(20Q13.12) WILD-TYPE   8 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 47(20Q13.12) MUTATED      5   95
  AMP PEAK 47(20Q13.12) WILD-TYPE    8  255
                        clus
vv                       AMP PEAK 47(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            95
                        clus
vv                       AMP PEAK 47(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             255
[1] 2 2
[1] FALSE

Clustering(48) Variable = AMP PEAK 48(20Q13.33) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 48(20Q13.33) MUTATED   113  24
  AMP PEAK 48(20Q13.33) WILD-TYPE 330  36
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                            137                             366 
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                             24                              36 
$`AMP PEAK 48(20Q13.33) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
      149.56        37.02        65.75        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       46.32        28.64         7.33        14.96         1.18         1.08 
TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        0.39         2.40         0.49         1.12         2.24         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A 
       22.26         0.92         0.76        16.87         1.71        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DO 
       57.80        45.53       125.42         3.39        97.71        31.30 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       41.95        18.25        53.92        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 
       13.55        20.28        12.43        76.83        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX 
       30.12        71.24        19.36         2.96         0.23         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.20        20.52         0.03         0.13         0.23         0.13 
TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
       80.38        43.13        44.71        17.85         4.11        75.72 
TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3F9 
       45.90        19.56       191.84       102.31        11.87       116.25 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT 
       33.11         5.03        34.95        36.49        30.81        24.39 
TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L 
       52.83        12.56        15.45         1.81        10.22        24.13 
TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 
       13.18         4.80        61.87        67.20        72.72        49.55 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J 
        8.55        22.55         4.44        37.32        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 
       31.07        18.67         1.41        28.08         0.72         2.07 
TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       41.42         4.11        35.38         9.37        12.39        91.96 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y 
       48.36        24.33        10.92        18.81        37.71        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GC 
       32.38        19.40        35.15        22.26         6.21         4.54 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A210 
        6.90        17.62        15.09         8.55         6.48        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
        3.62        14.40        13.45        29.10        27.35         6.44 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 
        3.72         5.88        40.01        59.01         9.07        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       41.06        45.01        23.97        12.92         7.00 

$`AMP PEAK 48(20Q13.33) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN 
      105.37        87.32        74.10        57.53        60.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K5 
       42.35        15.95         7.92         9.60         8.02         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BG 
        5.16         1.97        19.79         0.85         3.02         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68        14.66        22.49         1.28        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW 
        1.35        15.62         1.94        15.95         1.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        36.89         7.86        12.20 
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        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        35.01        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       19.20        15.25        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12        36.39        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       40.50        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.10         0.33         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       46.75        48.76        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       11.01         8.71       185.79       113.36        88.34        54.44 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU 
       16.73        19.50        18.41        17.36        16.57        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA 
       14.40        14.70        11.70        15.29        12.79        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        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        39.32        21.17        20.28        15.42        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       16.34        34.29        52.64        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        14.27         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A6W3 
        6.21        10.16        31.76        24.99        16.64        10.03 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG 
        9.86        46.95        23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79        29.95         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-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-A16X TCGA-D1-A16Y 
       27.42        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         6.77         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         3.52         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        31.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.01         7.36        16.80        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ 
       27.12        57.60        34.39        19.36        12.89        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       26.96        16.34        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO 
       23.34        23.34        23.90        22.78        13.97        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 
       18.84        17.88        16.11        12.43        15.81        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A547 
       18.87        22.82        45.76        31.04        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        2.14         6.97         5.29        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        28.93        28.96 
TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       25.02         1.74        13.15         2.43        10.82         9.11 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                         191.84                          185.79 
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                          18.81                           23.47 
[1] "0.0 - 191.8 (18.8)" "0.1 - 185.8 (23.5)"
[1] "hr=" "2"  
D48V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 48(20Q13.33) MUTATED                                        61
  AMP PEAK 48(20Q13.33) WILD-TYPE                                     319
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 48(20Q13.33) MUTATED                               6
  AMP PEAK 48(20Q13.33) WILD-TYPE                            15
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 48(20Q13.33) MUTATED                                  71
  AMP PEAK 48(20Q13.33) WILD-TYPE                                33
D48V3, multiclass
                                         clus
vv                                        AMP PEAK 48(20Q13.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            61
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  71
                                         clus
vv                                        AMP PEAK 48(20Q13.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             319
  MIXED SEROUS AND ENDOMETRIOID                                        15
  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"
D48V4, binary
                                 cls
clus                                0   1
  AMP PEAK 48(20Q13.33) MUTATED    24 114
  AMP PEAK 48(20Q13.33) WILD-TYPE 114 253
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 48(20Q13.33) MUTATED     24  114
  AMP PEAK 48(20Q13.33) WILD-TYPE  114  253
     clus
vv    AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE
  NO                             24                             114
  YES                           114                             253
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 48(20Q13.33) MUTATED    86   7  10  10
  AMP PEAK 48(20Q13.33) WILD-TYPE 265  15   7  20
D48V5, multiclass
    clus
vv   AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE
  R0                            86                             265
  R1                             7                              15
  R2                            10                               7
  RX                            10                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 48(20Q13.33) MUTATED                                  1     5
  AMP PEAK 48(20Q13.33) WILD-TYPE                                3    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 48(20Q13.33) MUTATED                          35
  AMP PEAK 48(20Q13.33) WILD-TYPE                        55
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 48(20Q13.33) MUTATED                                           3
  AMP PEAK 48(20Q13.33) WILD-TYPE                                         6
                                 vv
clus                              WHITE
  AMP PEAK 48(20Q13.33) MUTATED      87
  AMP PEAK 48(20Q13.33) WILD-TYPE   270
D48V6, multiclass
                                           clus
vv                                          AMP PEAK 48(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            35
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                87
                                           clus
vv                                          AMP PEAK 48(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              55
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  WHITE                                                                 270
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                 cls
clus                                0   1
  AMP PEAK 48(20Q13.33) MUTATED     4  95
  AMP PEAK 48(20Q13.33) WILD-TYPE   9 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 48(20Q13.33) MUTATED      4   95
  AMP PEAK 48(20Q13.33) WILD-TYPE    9  255
                        clus
vv                       AMP PEAK 48(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            95
                        clus
vv                       AMP PEAK 48(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             255
[1] 2 2
[1] FALSE

Clustering(49) Variable = AMP PEAK 49(22Q12.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 49(22Q12.2) MUTATED    43  14
  AMP PEAK 49(22Q12.2) WILD-TYPE 400  46
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            57                            446 
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            14                             46 
$`AMP PEAK 49(22Q12.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AP-A05A 
       37.02        28.64         1.18         0.85         0.49        39.42 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A1C8 TCGA-AX-A1CF 
      125.42         3.39        97.71        18.25        13.55        76.83 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A1MR TCGA-B5-A1MS 
        4.77        71.24         0.13        17.85       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       50.89         5.03        34.13         6.81        10.22        24.13 
TCGA-BS-A0TE TCGA-D1-A0ZP TCGA-D1-A16R TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
        4.80        29.95         0.69         6.77        13.22         0.72 
TCGA-DI-A1NN TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CH TCGA-EO-A3AS 
       35.38        24.33        10.92        37.71        19.40        34.39 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A3L3 
       23.90        19.27        15.09         3.62        13.45        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2EU 
       13.84         6.44         3.72        40.01        34.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-K6-A3WQ 
       59.01         9.07        28.93        25.02        41.06        13.15 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       23.97        12.92         7.00 

$`AMP PEAK 49(22Q12.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 
       36.33         9.60         8.02        91.04        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       19.79         2.40         3.02         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
        7.86        12.20        20.91        48.79       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       33.73         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        19.20        16.96        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       11.08        30.12        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        16.73        19.56        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       18.41        17.36        16.57        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        41.06        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
        6.21        10.16        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        23.47        85.55        78.21 
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 
       67.20        88.34        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        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65        18.67         1.41         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-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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        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-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
       16.01         7.36        16.80        18.81        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AU 
       33.01        27.12        57.60        24.79        32.38        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        12.89        27.16        26.96        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.34        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        17.62        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04        29.10        17.92         2.14         6.97 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.29         5.88        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 
        8.98        28.96        26.01        45.01         1.74         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       10.82         9.11        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                        191.84                         185.79 
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                        19.270                         22.965 
[1] "0.1 - 191.8 (19.3)" "0.0 - 185.8 (23.0)"
[1] "hr=" "2.5"
D49V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 49(22Q12.2) MUTATED                                        11
  AMP PEAK 49(22Q12.2) WILD-TYPE                                     369
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 49(22Q12.2) MUTATED                               2
  AMP PEAK 49(22Q12.2) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 49(22Q12.2) MUTATED                                  45
  AMP PEAK 49(22Q12.2) WILD-TYPE                                59
D49V3, multiclass
                                         clus
vv                                        AMP PEAK 49(22Q12.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           11
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 45
                                         clus
vv                                        AMP PEAK 49(22Q12.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            369
  MIXED SEROUS AND ENDOMETRIOID                                       19
  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"
D49V4, binary
                                cls
clus                               0   1
  AMP PEAK 49(22Q12.2) MUTATED    10  48
  AMP PEAK 49(22Q12.2) WILD-TYPE 128 319
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(22Q12.2) MUTATED     10   48
  AMP PEAK 49(22Q12.2) WILD-TYPE  128  319
     clus
vv    AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE
  NO                            10                            128
  YES                           48                            319
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 49(22Q12.2) MUTATED    32   3   7   6
  AMP PEAK 49(22Q12.2) WILD-TYPE 319  19  10  24
D49V5, multiclass
    clus
vv   AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE
  R0                           32                            319
  R1                            3                             19
  R2                            7                             10
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 49(22Q12.2) MUTATED                                  0     1
  AMP PEAK 49(22Q12.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 49(22Q12.2) MUTATED                          20
  AMP PEAK 49(22Q12.2) WILD-TYPE                        70
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 49(22Q12.2) MUTATED                                           0
  AMP PEAK 49(22Q12.2) WILD-TYPE                                         9
                                vv
clus                             WHITE
  AMP PEAK 49(22Q12.2) MUTATED      32
  AMP PEAK 49(22Q12.2) WILD-TYPE   325
D49V6, multiclass
                                           clus
vv                                          AMP PEAK 49(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               32
                                           clus
vv                                          AMP PEAK 49(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              9
  WHITE                                                                325
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                cls
clus                               0   1
  AMP PEAK 49(22Q12.2) MUTATED     2  40
  AMP PEAK 49(22Q12.2) WILD-TYPE  11 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(22Q12.2) MUTATED      2   40
  AMP PEAK 49(22Q12.2) WILD-TYPE   11  310
                        clus
vv                       AMP PEAK 49(22Q12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       AMP PEAK 49(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(50) Variable = AMP PEAK 50(XP11.23) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 50(XP11.23) MUTATED    69  13
  AMP PEAK 50(XP11.23) WILD-TYPE 374  47
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            82                            421 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            13                             47 
$`AMP PEAK 50(XP11.23) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GV TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3IA 
       65.75        20.81        91.04         0.49        22.26         0.92 
TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A05D TCGA-AP-A0LF 
       15.62        16.87         1.71         0.13        57.80         3.39 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW 
       33.40        31.30        41.95        16.24        68.35        37.78 
TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH 
       12.43        11.08        30.12        33.53        68.71        17.75 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A11R 
        0.13        56.91        43.13        23.01        17.88        33.50 
TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       27.35        50.89        34.13        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BK-A0C9 
       34.98        30.81        15.42        52.83        12.56        35.90 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       10.22        10.16        24.13         4.80        61.87        72.72 
TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 
       49.55        29.95        22.55         4.44         0.66        36.10 
TCGA-D1-A17R TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A2QY TCGA-E6-A1M0 
       11.15        41.42         8.48         4.11        91.96        17.06 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       10.92        24.79        34.39        26.96        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GX 
        6.21        23.34        17.88        17.62        15.09         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-FI-A2CY TCGA-FI-A2D4 
       19.33         3.62        29.10        27.35        34.98         7.99 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PV TCGA-K6-A3WQ 
       59.01         9.07        41.06        13.15 

$`AMP PEAK 50(XP11.23) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        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         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        2.24         1.68         1.64        14.66        22.49         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 
        1.87         2.33         0.99         2.70        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
        5.95        23.31        86.07         8.22        39.42        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89         7.86        12.20        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        63.16        36.36        97.71        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DP 
       49.22        25.08        71.67        60.36        55.89        35.54 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 
       49.15         6.71        30.90        10.42        27.85        18.25 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       33.73         0.56        13.58        19.82        29.69        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        20.28        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       71.24        61.18        33.40        40.50        19.36        26.33 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JS 
        0.23         1.18         8.35        14.47        80.38        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       30.51        25.91        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       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        45.90        43.96        40.50        36.82        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 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       15.29        12.79       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11         5.03        41.06        34.95        18.61        20.19 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        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        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       20.12        11.31         6.81        34.98         6.21        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-A0TJ TCGA-BS-A0U5 
       23.47        85.55        78.21        77.95        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        67.20        88.34        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        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       28.67        23.93         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-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-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 
        1.41         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         6.77         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-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         3.52        44.88         0.26         4.27 
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-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 
        9.37        12.39        31.10        23.38        48.36         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        6.67        24.33        16.01         7.36        16.80        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       32.38        19.40        19.36        35.15        12.89        27.16 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 
       16.11        12.43        15.81         8.55        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       18.87        22.82        13.45        45.76        31.04        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
        6.44        17.92         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.88        40.01        33.99        36.00        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       96.69        28.93        28.96        25.02        26.01        45.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        1.74         2.43        10.82         9.11        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                         91.96                         191.84 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                        22.405                         22.920 
[1] "0.1 - 92.0 (22.4)"  "0.0 - 191.8 (22.9)"
[1] "hr=" "1.5"
D50V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 50(XP11.23) MUTATED                                        49
  AMP PEAK 50(XP11.23) WILD-TYPE                                     331
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 50(XP11.23) MUTATED                               4
  AMP PEAK 50(XP11.23) WILD-TYPE                            17
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 50(XP11.23) MUTATED                                  29
  AMP PEAK 50(XP11.23) WILD-TYPE                                75
D50V3, multiclass
                                         clus
vv                                        AMP PEAK 50(XP11.23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           49
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 29
                                         clus
vv                                        AMP PEAK 50(XP11.23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            331
  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"
D50V4, binary
                                cls
clus                               0   1
  AMP PEAK 50(XP11.23) MUTATED    15  67
  AMP PEAK 50(XP11.23) WILD-TYPE 123 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(XP11.23) MUTATED     15   67
  AMP PEAK 50(XP11.23) WILD-TYPE  123  300
     clus
vv    AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE
  NO                            15                            123
  YES                           67                            300
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 50(XP11.23) MUTATED    58   3   5   5
  AMP PEAK 50(XP11.23) WILD-TYPE 293  19  12  25
D50V5, multiclass
    clus
vv   AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE
  R0                           58                            293
  R1                            3                             19
  R2                            5                             12
  RX                            5                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 50(XP11.23) MUTATED                                  0     2
  AMP PEAK 50(XP11.23) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 50(XP11.23) MUTATED                          14
  AMP PEAK 50(XP11.23) WILD-TYPE                        76
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  AMP PEAK 50(XP11.23) MUTATED                                           1
  AMP PEAK 50(XP11.23) WILD-TYPE                                         8
                                vv
clus                             WHITE
  AMP PEAK 50(XP11.23) MUTATED      58
  AMP PEAK 50(XP11.23) WILD-TYPE   299
D50V6, multiclass
                                           clus
vv                                          AMP PEAK 50(XP11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               58
                                           clus
vv                                          AMP PEAK 50(XP11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                299
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                               0   1
  AMP PEAK 50(XP11.23) MUTATED     1  60
  AMP PEAK 50(XP11.23) WILD-TYPE  12 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(XP11.23) MUTATED      1   60
  AMP PEAK 50(XP11.23) WILD-TYPE   12  290
                        clus
vv                       AMP PEAK 50(XP11.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       AMP PEAK 50(XP11.23) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(51) Variable = AMP PEAK 51(XQ28) MUTATION ANALYSIS
D51V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 51(XQ28) MUTATED    64  18
  AMP PEAK 51(XQ28) WILD-TYPE 379  42
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         82                         421 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         18                          42 
$`AMP PEAK 51(XQ28) MUTATED`
TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BF TCGA-AJ-A3NG TCGA-AJ-A8CW 
       20.81        14.96         1.08         1.12        15.62         0.13 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LO 
        5.95        39.42        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        41.95        16.24        33.73        68.35         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A3G3 TCGA-AX-A3G4 
       30.12        33.53        68.71        17.75         0.03         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A11R TCGA-B5-A11S 
       80.38        56.91        43.13        23.01        33.50        27.35 
TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       11.87         5.03        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BK-A0C9 
        7.92        30.81        15.42        52.83        12.56        35.90 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT 
       10.22        24.13        16.64         4.80        61.87        72.72 
TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A16R TCGA-D1-A17R 
       49.55         4.44         0.66        36.10         0.69        11.15 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
       41.42         8.48         4.11        12.39        91.96        48.36 
TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AV 
       17.06        24.33        37.71        24.79        19.40        35.15 
TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GX 
       22.26         6.21        23.34        17.88        17.62         6.48 
TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY 
       19.33        14.40        27.35        17.92         5.88        34.98 
TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KJ-A3U4 
        7.99        26.01        45.01         2.43 

$`AMP PEAK 51(XQ28) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        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        19.96        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         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.33         5.16         7.33         1.18         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         0.49         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH 
        1.28         0.92        36.99        20.65         1.35         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        0.99         2.70        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
        8.22        57.80         7.86        12.20        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       35.54        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       18.25         0.56        13.58        19.82        29.69        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39        11.08        71.24        61.18        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JS 
        0.23         1.18         8.35        14.47         0.13        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       32.09        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14        33.11        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       20.19        38.37        36.49        28.27        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        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       20.28        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31         6.81        34.98         6.21        10.16 
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-A0TJ TCGA-BS-A0U5 
       23.47        85.55        78.21        77.95        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        67.20        88.34        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        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        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-A167 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       32.58        15.72        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-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         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         6.77         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-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-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-A2G7 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52        44.88         0.26 
TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 
       35.38         9.37        31.10        23.38         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.01         7.36        16.80        10.92        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS 
       35.05        33.01        27.12        57.60        32.38        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G8 
       19.36        12.89        27.16        26.96        16.34        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
        4.54         8.15        24.36        27.16        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS 
       22.78        13.97         6.90        19.27        18.84        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
       16.11        12.43        15.81         8.55        12.59         3.62 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        13.45        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84         6.44         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        33.99        36.00        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV 
       59.01         9.07        28.93        28.96        25.02        41.06 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        1.74        13.15        10.82         9.11        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                      91.96                      191.84 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                      21.60                       22.92 
[1] "0.0 - 92.0 (21.6)"  "0.1 - 191.8 (22.9)"
[1] "hr=" "2.4"
D51V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 51(XQ28) MUTATED                                        51
  AMP PEAK 51(XQ28) WILD-TYPE                                     329
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  AMP PEAK 51(XQ28) MUTATED                               3
  AMP PEAK 51(XQ28) WILD-TYPE                            18
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 51(XQ28) MUTATED                                  29
  AMP PEAK 51(XQ28) WILD-TYPE                                75
D51V3, multiclass
                                         clus
vv                                        AMP PEAK 51(XQ28) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        51
  MIXED SEROUS AND ENDOMETRIOID                                   3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              29
                                         clus
vv                                        AMP PEAK 51(XQ28) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         329
  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"
D51V4, binary
                             cls
clus                            0   1
  AMP PEAK 51(XQ28) MUTATED    22  61
  AMP PEAK 51(XQ28) WILD-TYPE 116 306
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 51(XQ28) MUTATED     22   61
  AMP PEAK 51(XQ28) WILD-TYPE  116  306
     clus
vv    AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE
  NO                         22                         116
  YES                        61                         306
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 51(XQ28) MUTATED    60   2   6   5
  AMP PEAK 51(XQ28) WILD-TYPE 291  20  11  25
D51V5, multiclass
    clus
vv   AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE
  R0                        60                         291
  R1                         2                          20
  R2                         6                          11
  RX                         5                          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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 51(XQ28) MUTATED                                  1     2
  AMP PEAK 51(XQ28) WILD-TYPE                                3    17
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK 51(XQ28) MUTATED                          18
  AMP PEAK 51(XQ28) WILD-TYPE                        72
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 51(XQ28) MUTATED                                           2    55
  AMP PEAK 51(XQ28) WILD-TYPE                                         7   302
D51V6, multiclass
                                           clus
vv                                          AMP PEAK 51(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             2
  BLACK OR AFRICAN AMERICAN                                        18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            55
                                           clus
vv                                          AMP PEAK 51(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                          72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             302
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                             cls
clus                            0   1
  AMP PEAK 51(XQ28) MUTATED     3  55
  AMP PEAK 51(XQ28) WILD-TYPE  10 295
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 51(XQ28) MUTATED      3   55
  AMP PEAK 51(XQ28) WILD-TYPE   10  295
                        clus
vv                       AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             3                          10
  NOT HISPANIC OR LATINO                        55                         295
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK  1(1P36.21) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.21) MUTATED    55   9
  DEL PEAK  1(1P36.21) WILD-TYPE 388  51
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            64                            439 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                             9                             51 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M 
      149.56        37.02        60.53        36.33        46.32         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A6NU 
        1.97         0.39         0.49         0.76        16.87         0.99 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AW-A1PO 
       57.80        45.53        36.89        48.79       125.42         0.56 
TCGA-AX-A06B TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A1CP 
       53.92        13.55        20.28        76.83        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3FX TCGA-B5-A0JN TCGA-B5-A11I 
       11.08         4.77         2.96         0.13        80.38        75.72 
TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BS-A0V8 
       36.82        11.87        12.79        34.13        36.49        49.55 
TCGA-D1-A0ZQ TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 
        8.55        11.51        29.92        31.07        18.67         6.77 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y8 
        2.07        44.88         4.27        12.39        91.96        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         6.90        19.27        18.84 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A4KR TCGA-EY-A72D TCGA-FI-A2F8 
       12.59        14.40        45.76         6.44         5.88        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A7D5 
       26.01        45.01         1.74        23.97 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD 
        1.08       106.88        83.51        17.85        32.78         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
      105.37        87.32        74.10        57.53        65.75        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        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-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       91.04        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.08        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87         1.71         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        39.42         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
      117.99       110.37         3.39        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 
       38.70         0.23         0.10         0.33         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.03         0.13         0.23         1.18         8.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.13        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
        4.11         8.71       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 
       45.90        43.96        40.50        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       15.29       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       10.22        10.16        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        23.47        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        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79        29.95         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A16O TCGA-D1-A16Q 
       36.36        37.51        36.79        27.42        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         1.41         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-A1O5 
       13.22         0.72        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
        1.05         3.95         3.52        41.42         8.48         0.26 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       35.38         9.37        31.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        24.33        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        18.81        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        24.79        32.38        19.40        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       12.89        26.96        22.26         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       22.78        13.97        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       12.43        15.81         8.55         6.48        19.33         3.62 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        13.45        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        17.92         2.14         6.97         3.72         5.29 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
        8.98        96.69        59.01         9.07        28.93        28.96 
TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
       41.06        13.15         2.43        10.82         9.11        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        149.56                         191.84 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        22.125                         22.820 
[1] "0.1 - 149.6 (22.1)" "0.0 - 191.8 (22.8)"
[1] "hr=" "1.2"
D52V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                        26
  DEL PEAK  1(1P36.21) WILD-TYPE                                     354
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  1(1P36.21) MUTATED                               5
  DEL PEAK  1(1P36.21) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                  33
  DEL PEAK  1(1P36.21) WILD-TYPE                                71
D52V3, multiclass
                                         clus
vv                                        DEL PEAK  1(1P36.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           26
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 33
                                         clus
vv                                        DEL PEAK  1(1P36.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            354
  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"
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    18  46
  DEL PEAK  1(1P36.21) WILD-TYPE 120 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     18   46
  DEL PEAK  1(1P36.21) WILD-TYPE  120  321
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            18                            120
  YES                           46                            321
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.21) MUTATED    46   5   2   2
  DEL PEAK  1(1P36.21) WILD-TYPE 305  17  15  28
D52V5, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  R0                           46                            305
  R1                            5                             17
  R2                            2                             15
  RX                            2                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.21) MUTATED                                  1     1
  DEL PEAK  1(1P36.21) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.21) MUTATED                          18
  DEL PEAK  1(1P36.21) WILD-TYPE                        72
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  1(1P36.21) MUTATED                                           1
  DEL PEAK  1(1P36.21) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK  1(1P36.21) MUTATED      39
  DEL PEAK  1(1P36.21) WILD-TYPE   318
D52V6, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               39
                                           clus
vv                                          DEL PEAK  1(1P36.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED     3  40
  DEL PEAK  1(1P36.21) WILD-TYPE  10 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED      3   40
  DEL PEAK  1(1P36.21) WILD-TYPE   10  310
                        clus
vv                       DEL PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK  2(1P36.11) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  2(1P36.11) MUTATED    61  13
  DEL PEAK  2(1P36.11) WILD-TYPE 382  47
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            74                            429 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            13                             47 
$`DEL PEAK  2(1P36.11) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M 
      149.56        60.53        36.33        46.32        14.96         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
        1.97         0.39         0.49         0.92         0.76        16.87 
TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI 
        1.71        57.80        45.53        36.89        48.79        97.71 
TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF 
        0.56        53.92        16.96        13.55        20.28        76.83 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HG TCGA-AX-A3FX 
       36.39        11.08        30.12        71.24        26.33         0.13 
TCGA-AX-A3G3 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
        0.03        75.72        36.82        11.87        12.79         5.03 
TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A16N 
       34.13        36.49        12.56        49.55         8.55        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G7 
       18.67         1.41         6.77        13.22         2.07        44.88 
TCGA-D1-A3DG TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EO-A1Y8 TCGA-EO-A3AS TCGA-EO-A3AZ 
        4.27         9.37        12.39        37.71        34.39        27.16 
TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A210 TCGA-EY-A212 
       16.34         6.90        19.27        18.84        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       14.40        13.45        45.76        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
        6.44        28.93        25.02        41.06        45.01         1.74 
TCGA-K6-A3WQ TCGA-PG-A7D5 
       13.15        23.97 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        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         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        91.04        28.64         5.33         5.16         7.33 
TCGA-AJ-A23N TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        1.08        19.79         0.85         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         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         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.94        15.95         1.87         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
        8.22        39.42         7.86        12.20        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        18.25        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC 
       40.11        65.88        13.28        19.20        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       20.05        72.56        54.12        67.50        25.12         4.77 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.10         0.33         0.20        20.52         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        14.40        14.70        11.70        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        78.81        62.14        33.11        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 
       35.67        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        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 
       23.47        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        67.20        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       29.95         0.56         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48         0.26         4.11        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30        35.38        31.10        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        24.33        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        18.81        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       33.01        27.12        57.60        24.79        32.38        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       19.36        35.15        12.89        26.96        22.26         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.34        23.90        22.78        13.97        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A547 TCGA-EY-A548 
       19.33        18.87        22.82        31.04        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        6.97         3.72         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-KJ-A3U4 TCGA-PG-A5BC 
       59.01         9.07        28.96        26.01         2.43        10.82 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                        149.56                         191.84 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                        17.815                         23.310 
[1] "0.0 - 149.6 (17.8)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.8"
D53V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                                        24
  DEL PEAK  2(1P36.11) WILD-TYPE                                     356
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  2(1P36.11) MUTATED                               5
  DEL PEAK  2(1P36.11) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                                  45
  DEL PEAK  2(1P36.11) WILD-TYPE                                59
D53V3, multiclass
                                         clus
vv                                        DEL PEAK  2(1P36.11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           24
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 45
                                         clus
vv                                        DEL PEAK  2(1P36.11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            356
  MIXED SEROUS AND ENDOMETRIOID                                       16
  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"
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    18  56
  DEL PEAK  2(1P36.11) WILD-TYPE 120 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     18   56
  DEL PEAK  2(1P36.11) WILD-TYPE  120  311
     clus
vv    DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  NO                            18                            120
  YES                           56                            311
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  2(1P36.11) MUTATED    49   7   5   2
  DEL PEAK  2(1P36.11) WILD-TYPE 302  15  12  28
D53V5, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                           49                            302
  R1                            7                             15
  R2                            5                             12
  RX                            2                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P36.11) MUTATED                                  1     1
  DEL PEAK  2(1P36.11) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P36.11) MUTATED                          19
  DEL PEAK  2(1P36.11) WILD-TYPE                        71
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  2(1P36.11) MUTATED                                           1
  DEL PEAK  2(1P36.11) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK  2(1P36.11) MUTATED      48
  DEL PEAK  2(1P36.11) WILD-TYPE   309
D53V6, multiclass
                                           clus
vv                                          DEL PEAK  2(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               48
                                           clus
vv                                          DEL PEAK  2(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                309
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED     4  50
  DEL PEAK  2(1P36.11) WILD-TYPE   9 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      4   50
  DEL PEAK  2(1P36.11) WILD-TYPE    9  300
                        clus
vv                       DEL PEAK  2(1P36.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       DEL PEAK  2(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            300
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    20   5
  DEL PEAK  3(2P25.3) WILD-TYPE 423  55
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           25                           478 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                            5                            55 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-A5-A0GR TCGA-A5-A1OG TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AP-A0L9 
       36.82        11.44         2.24        22.26         0.92       125.42 
TCGA-AW-A1PO TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2HK TCGA-AX-A3FX TCGA-AX-A3G3 
        0.56        12.43        76.83         2.96         0.13         0.03 
TCGA-B5-A3FD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16R TCGA-D1-A1NW 
       33.11        67.20        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        13.45        28.93         1.74        10.82 
TCGA-PG-A914 
       12.92 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       65.75        60.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        1.28        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89         7.86        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        18.25        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       27.39        30.02        60.66        35.01        28.54        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        20.28        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.23         0.10         0.33         0.20        20.52         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB 
       17.88        13.74        17.10        17.85        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       11.70        11.87        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       78.81        62.14         5.03        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93         1.74         4.44        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-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        27.16        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 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       24.33        16.01         7.36        16.80        18.81        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       32.38        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
        8.55         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       18.87        22.82        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84         6.44        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        5.29         5.88        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       28.96        25.02        26.01        41.06        45.01        13.15 
TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
        2.43         9.11        23.97         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                        11.44                         23.36 
[1] "0.0 - 125.4 (11.4)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.6"
D54V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                        12
  DEL PEAK  3(2P25.3) WILD-TYPE                                     368
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  3(2P25.3) MUTATED                               2
  DEL PEAK  3(2P25.3) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                  11
  DEL PEAK  3(2P25.3) WILD-TYPE                                93
D54V3, multiclass
                                         clus
vv                                        DEL PEAK  3(2P25.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          12
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                11
                                         clus
vv                                        DEL PEAK  3(2P25.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           368
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V4, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     3  22
  DEL PEAK  3(2P25.3) WILD-TYPE 135 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      3   22
  DEL PEAK  3(2P25.3) WILD-TYPE  135  345
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                            3                           135
  YES                          22                           345
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2P25.3) MUTATED    17   0   2   2
  DEL PEAK  3(2P25.3) WILD-TYPE 334  22  15  28
D54V5, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          17                           334
  R1                           0                            22
  R2                           2                            15
  RX                           2                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2P25.3) MUTATED                                  0     1
  DEL PEAK  3(2P25.3) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(2P25.3) MUTATED                           7
  DEL PEAK  3(2P25.3) WILD-TYPE                        83
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2P25.3) MUTATED                                           1    15
  DEL PEAK  3(2P25.3) WILD-TYPE                                         8   342
D54V6, multiclass
                                           clus
vv                                          DEL PEAK  3(2P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                           7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              15
                                           clus
vv                                          DEL PEAK  3(2P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     0  19
  DEL PEAK  3(2P25.3) WILD-TYPE  13 331
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      0   19
  DEL PEAK  3(2P25.3) WILD-TYPE   13  331
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           331
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    29  15
  DEL PEAK  4(2Q22.1) WILD-TYPE 414  45
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           44                           459 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           15                            45 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 
        1.18         0.49         1.12        16.87         1.71        21.99 
TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CR 
       45.53       125.42        33.73         0.56        37.78        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A3G1 TCGA-B5-A0JN TCGA-B5-A1MS TCGA-B5-A1MY 
        4.77        30.12        20.52        80.38       102.31        11.87 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BS-A0TE 
        5.03        34.13        15.45         6.81        10.16         4.80 
TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NO 
       67.20        11.51         2.07         4.27         4.11         9.37 
TCGA-EO-A1Y7 TCGA-EO-A2CH TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A212 
       18.81        19.40         4.54        17.62         8.55         3.62 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A3PV TCGA-H5-A2HR 
       13.45        29.10        13.84         6.44        41.06         1.74 
TCGA-PG-A5BC TCGA-PG-A915 
       10.82         7.00 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       11.44        36.33         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       28.64         5.33         5.16         7.33        14.96         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26         1.28         0.92        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW 
       15.62         0.76         1.94        15.95         1.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        0.99         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91        48.79       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        18.25        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       19.20        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        38.70         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.13        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       78.81        62.14        33.11        41.06        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       38.37        36.49        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 
       52.64        52.83        56.58        14.83        12.56        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
        6.21        10.22        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        23.47        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        88.34        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        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         1.41         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         6.77 
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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ 
        3.52        41.42         8.48        44.88         0.26        27.16 
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-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        32.38        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       27.16        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       12.59        14.40        18.87        22.82        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        17.92         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.96        25.02        26.01        45.01        13.15         2.43 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.49                          0.03 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       11.295                        23.900 
[1] "0.5 - 125.4 (11.3)" "0.0 - 191.8 (23.9)"
[1] "hr=" "5"  
D55V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                        16
  DEL PEAK  4(2Q22.1) WILD-TYPE                                     364
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  4(2Q22.1) MUTATED                               2
  DEL PEAK  4(2Q22.1) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                  26
  DEL PEAK  4(2Q22.1) WILD-TYPE                                78
D55V3, multiclass
                                         clus
vv                                        DEL PEAK  4(2Q22.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          16
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                26
                                         clus
vv                                        DEL PEAK  4(2Q22.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           364
  MIXED SEROUS AND ENDOMETRIOID                                      19
  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"
D55V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     4  40
  DEL PEAK  4(2Q22.1) WILD-TYPE 134 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      4   40
  DEL PEAK  4(2Q22.1) WILD-TYPE  134  327
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            4                           134
  YES                          40                           327
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED    24   2   5   6
  DEL PEAK  4(2Q22.1) WILD-TYPE 327  20  12  24
D55V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                          24                           327
  R1                           2                            20
  R2                           5                            12
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q22.1) MUTATED                                  0     1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q22.1) MUTATED                          15
  DEL PEAK  4(2Q22.1) WILD-TYPE                        75
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q22.1) MUTATED                                           1    25
  DEL PEAK  4(2Q22.1) WILD-TYPE                                         8   332
D55V6, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              25
                                           clus
vv                                          DEL PEAK  4(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               332
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     1  32
  DEL PEAK  4(2Q22.1) WILD-TYPE  12 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1   32
  DEL PEAK  4(2Q22.1) WILD-TYPE   12  318
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           318
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D56V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.3) MUTATED    40   9
  DEL PEAK  5(2Q37.3) WILD-TYPE 403  51
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           49                           454 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                            9                            51 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
       36.82        36.33        91.04         0.49         0.76         2.24 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
       22.26         1.28         0.92         1.35        16.87         1.71 
TCGA-AP-A05A TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A1CF TCGA-AX-A2H4 
       39.42        97.71        18.25         0.56        76.83        30.12 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A0KB TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-BG-A0M8 
        0.13        20.52         4.11       102.31        12.79        36.49 
TCGA-BG-A18C TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A16G 
       15.45        61.87        67.20        49.55        29.95        27.42 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-EO-A1Y5 
       28.08        13.22         2.07         9.37        48.36        10.92 
TCGA-EO-A1Y7 TCGA-EO-A3AS TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GR 
       18.81        34.39        16.34         4.54        23.90        17.62 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A3PV TCGA-PG-A7D5 
       15.81         8.55        29.10         3.72        41.06        23.97 
TCGA-PG-A915 
        7.00 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       65.75        60.53        60.53        46.55        38.37        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BK 
       19.79         0.85         2.40         3.02         1.12         1.68 
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-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU 
        0.76         1.94        15.95         1.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        57.80        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        33.73        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.33         0.20         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 
       14.40        14.70        11.70        11.87        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98         7.92        38.37        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       12.56        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
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        23.47        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        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
        1.74         4.44        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-A16I 
       36.10        37.32        36.36        37.51        36.79        11.51 
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 
        1.41         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         6.77         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 
       35.38        12.39        31.10        91.96        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        24.33        16.01         7.36        16.80 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        32.38        19.40        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       27.16        26.96        22.26         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        19.27        18.84        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       12.43         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        13.45        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       13.84         6.44        17.92         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.96        25.02        26.01        45.01         1.74        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
        2.43        10.82         9.11        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       102.31                        191.84 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        18.25                         23.26 
[1] "0.1 - 102.3 (18.2)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.9"
D56V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                        25
  DEL PEAK  5(2Q37.3) WILD-TYPE                                     355
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  5(2Q37.3) MUTATED                               2
  DEL PEAK  5(2Q37.3) WILD-TYPE                            19
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                  22
  DEL PEAK  5(2Q37.3) WILD-TYPE                                82
D56V3, multiclass
                                         clus
vv                                        DEL PEAK  5(2Q37.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          25
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                22
                                         clus
vv                                        DEL PEAK  5(2Q37.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           355
  MIXED SEROUS AND ENDOMETRIOID                                      19
  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"
D56V4, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     9  40
  DEL PEAK  5(2Q37.3) WILD-TYPE 129 327
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      9   40
  DEL PEAK  5(2Q37.3) WILD-TYPE  129  327
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                            9                           129
  YES                          40                           327
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.3) MUTATED    32   2   3   7
  DEL PEAK  5(2Q37.3) WILD-TYPE 319  20  14  23
D56V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                          32                           319
  R1                           2                            20
  R2                           3                            14
  RX                           7                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q37.3) MUTATED                                  0     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q37.3) MUTATED                          13
  DEL PEAK  5(2Q37.3) WILD-TYPE                        77
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q37.3) MUTATED                                           2    30
  DEL PEAK  5(2Q37.3) WILD-TYPE                                         7   327
D56V6, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              30
                                           clus
vv                                          DEL PEAK  5(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            77
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     1  38
  DEL PEAK  5(2Q37.3) WILD-TYPE  12 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      1   38
  DEL PEAK  5(2Q37.3) WILD-TYPE   12  312
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           312
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK  6(3P14.2) MUTATION ANALYSIS
D57V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P14.2) MUTATED    58  11
  DEL PEAK  6(3P14.2) WILD-TYPE 385  49
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           69                           434 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           11                            49 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A2QN 
       37.02        11.44        36.33        46.32         1.18         2.40 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
        1.12         1.64         1.35         1.71         0.99        21.99 
TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO 
       57.80       125.42        97.71        41.95        18.25         0.56 
TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 
       53.92        37.78        76.83        36.39        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN 
       71.24        61.18        19.36         0.03         0.13        80.38 
TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1N2 TCGA-BG-A0M6 TCGA-BG-A0YV 
       23.01         4.11        75.72        12.79         7.92        12.56 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-D1-A0ZZ 
       15.45         6.81        10.16        16.64        61.87        22.55 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-DI-A1NN 
       31.07        18.67         0.72         2.07        44.88        35.38 
TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A2CH TCGA-EO-A3KW 
       31.10        48.36        10.92        18.81        19.40        16.34 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A2OQ 
       23.90        19.27        18.84        17.62        15.81        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EX 
       27.35        13.84         6.44         3.72        36.00         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-PG-A915 
       28.93        25.02         7.00 

$`DEL PEAK  6(3P14.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        91.04        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
       14.96         1.08         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
        3.02         0.49         0.76         2.24         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        2.33         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        45.53        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        20.91        48.79       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR 
       71.67        60.36        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        30.90        10.42        27.85        16.24        33.73 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F 
       35.34        45.99        66.58        34.98        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       67.50        25.12        30.12        33.53        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       40.50        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.13         0.23         1.18         8.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 
      116.25        96.30        78.81        62.14        33.11         5.03 
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-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 
       14.83        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        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         6.21        10.22        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        23.47 
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-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       30.74        97.41        67.20        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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         1.41         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         6.77 
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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
       41.42         8.48         0.26         4.27         4.11        27.16 
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-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       91.96        23.38        17.06         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.01         7.36        16.80        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       33.01        27.12        57.60        24.79        32.38        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.36        35.15        12.89        27.16        26.96        22.26 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ 
       23.34        23.34        22.78        13.97         6.90        17.88 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59         3.62        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       45.76        31.04        17.92         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        34.98        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV 
        8.98        96.69        59.01        28.96        26.01        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       45.01         1.74        13.15         2.43        10.82         9.11 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.97        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       18.810                        23.425 
[1] "0.0 - 125.4 (18.8)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.6"
D57V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                        23
  DEL PEAK  6(3P14.2) WILD-TYPE                                     357
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  6(3P14.2) MUTATED                               6
  DEL PEAK  6(3P14.2) WILD-TYPE                            15
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                  40
  DEL PEAK  6(3P14.2) WILD-TYPE                                64
D57V3, multiclass
                                         clus
vv                                        DEL PEAK  6(3P14.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          23
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                40
                                         clus
vv                                        DEL PEAK  6(3P14.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           357
  MIXED SEROUS AND ENDOMETRIOID                                      15
  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"
D57V4, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    16  53
  DEL PEAK  6(3P14.2) WILD-TYPE 122 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     16   53
  DEL PEAK  6(3P14.2) WILD-TYPE  122  314
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                           16                           122
  YES                          53                           314
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P14.2) MUTATED    50   3   4   4
  DEL PEAK  6(3P14.2) WILD-TYPE 301  19  13  26
D57V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  R0                          50                           301
  R1                           3                            19
  R2                           4                            13
  RX                           4                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P14.2) MUTATED                                  0     1
  DEL PEAK  6(3P14.2) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(3P14.2) MUTATED                          21
  DEL PEAK  6(3P14.2) WILD-TYPE                        69
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(3P14.2) MUTATED                                           0    43
  DEL PEAK  6(3P14.2) WILD-TYPE                                         9   314
D57V6, multiclass
                                           clus
vv                                          DEL PEAK  6(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              43
                                           clus
vv                                          DEL PEAK  6(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            69
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               314
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED     0  50
  DEL PEAK  6(3P14.2) WILD-TYPE  13 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      0   50
  DEL PEAK  6(3P14.2) WILD-TYPE   13  300
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          50
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           300
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK  7(3Q13.31) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(3Q13.31) MUTATED    37   3
  DEL PEAK  7(3Q13.31) WILD-TYPE 406  57
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            40                            463 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                             3                             57 
$`DEL PEAK  7(3Q13.31) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A2QK TCGA-AJ-A3EM 
       37.02        11.44        36.33        91.04         0.39        22.26 
TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LJ TCGA-AP-A1DQ TCGA-AP-A5FX 
        1.71        45.53       125.42        31.73        41.95        33.73 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A2H8 TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.56        37.78        20.28        61.18        20.52         0.13 
TCGA-AX-A3G7 TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11W TCGA-B5-A5OD 
        0.23        80.38        17.85       185.79        19.50        34.13 
TCGA-BG-A3PP TCGA-BK-A0CB TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A16I TCGA-D1-A16S 
        6.81         6.21        24.13        16.64        11.51        18.67 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-E6-A1LZ TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GO 
        2.07         4.11        48.36        34.39        27.16        19.27 
TCGA-EY-A1GP TCGA-EY-A2OQ TCGA-FI-A2D2 TCGA-H5-A2HR 
       18.84        29.10        36.00         1.74 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM 
       14.96         1.18         1.08         1.97        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40         3.02         0.49         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68         1.64        14.66        22.49         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       36.99        20.65         1.35        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95         1.87        16.87         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91        48.79       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        97.71        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        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-AX-A05S 
       30.90        10.42        27.85        16.24        18.25        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       67.50        25.12        36.39        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       71.24        33.53        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 
        0.23         0.10         0.33         0.13         0.20         0.03 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47         0.13        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         4.11         8.71       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        45.90        43.96        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11Y 
       32.09        33.50        27.35        16.73        19.56        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV 
       17.36        16.57       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.70        11.70        11.87        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98         7.92        38.37        36.49        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C 
       12.56        13.78        14.73        14.01        15.45        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98        10.22        10.16        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        23.47 
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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        24.33        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        57.60        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.40        19.36        35.15        12.89        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       16.34         6.21        14.99         4.54         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81         8.55         6.48        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84         6.44        17.92         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        3.72         5.29         5.88        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        7.99        13.84         8.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       28.93        28.96        25.02        26.01        41.06        45.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       13.15         2.43        10.82         9.11        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        185.79                         191.84 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                         21.39                          22.92 
[1] "0.1 - 185.8 (21.4)" "0.0 - 191.8 (22.9)"
[1] "hr=" "1.7"
D58V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  7(3Q13.31) MUTATED                                        17
  DEL PEAK  7(3Q13.31) WILD-TYPE                                     363
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  7(3Q13.31) MUTATED                               3
  DEL PEAK  7(3Q13.31) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  7(3Q13.31) MUTATED                                  20
  DEL PEAK  7(3Q13.31) WILD-TYPE                                84
D58V3, multiclass
                                         clus
vv                                        DEL PEAK  7(3Q13.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           17
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 20
                                         clus
vv                                        DEL PEAK  7(3Q13.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            363
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     8  32
  DEL PEAK  7(3Q13.31) WILD-TYPE 130 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      8   32
  DEL PEAK  7(3Q13.31) WILD-TYPE  130  335
     clus
vv    DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  NO                             8                            130
  YES                           32                            335
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  7(3Q13.31) MUTATED    28   1   0   2
  DEL PEAK  7(3Q13.31) WILD-TYPE 323  21  17  28
D58V5, multiclass
    clus
vv   DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  R0                           28                            323
  R1                            1                             21
  R2                            0                             17
  RX                            2                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q13.31) MUTATED                                  0     1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(3Q13.31) MUTATED                           9
  DEL PEAK  7(3Q13.31) WILD-TYPE                        81
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK  7(3Q13.31) MUTATED                                           1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK  7(3Q13.31) MUTATED      27
  DEL PEAK  7(3Q13.31) WILD-TYPE   330
D58V6, multiclass
                                           clus
vv                                          DEL PEAK  7(3Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                            9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               27
                                           clus
vv                                          DEL PEAK  7(3Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                330
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     1  24
  DEL PEAK  7(3Q13.31) WILD-TYPE  12 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      1   24
  DEL PEAK  7(3Q13.31) WILD-TYPE   12  326
                        clus
vv                       DEL PEAK  7(3Q13.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK  7(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            326
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK  8(4P16.3) MUTATION ANALYSIS
D59V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4P16.3) MUTATED    65  16
  DEL PEAK  8(4P16.3) WILD-TYPE 378  44
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           81                           422 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           16                            44 
$`DEL PEAK  8(4P16.3) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 
      149.56        60.53        36.82        19.96        91.04        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF 
        7.33        14.96         0.39         0.49         1.64         1.35 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H 
        0.76        16.87         1.71         5.95        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B 
       36.89         3.39        33.40        18.25         0.56        53.92 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 
       37.78        16.96        20.28        12.43        11.08        30.12 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0JX 
       19.36         2.96         0.23        20.52         0.13        44.71 
TCGA-B5-A0K8 TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-BG-A0M8 
       17.85        88.34        75.72        36.82        11.87        36.49 
TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       12.56         6.81        24.13        61.87        67.20        49.55 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU 
       39.48        37.32        18.67         1.41         6.77        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A1Y7 TCGA-EO-A3AZ 
        0.72        18.25        35.38        12.39        18.81        27.16 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A212 
       22.26        16.34        19.27        18.84        17.62         3.62 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2EX 
       14.40        13.45        45.76        27.35         6.44         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       28.93        25.02        26.01        41.06        45.01        13.15 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       10.82        23.97         7.00 

$`DEL PEAK  8(4P16.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        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-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       46.32         5.33         5.16         1.18         1.08         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        2.24         1.68        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        0.92        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.87         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
       21.99        23.31        86.07         8.22        39.42         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        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 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        36.39         4.77        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       68.71        33.40        40.50        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13        38.70         0.10         0.33         0.13         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.03         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      185.79       113.36        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.40        14.70        11.70        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98         7.92        38.37        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        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-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        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         6.21        10.22        10.16        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 
       23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        4.27         4.11        27.16        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        91.96        23.38        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        24.33        16.01         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        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.12        57.60        24.79        32.38        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 
       19.36        35.15        12.89        26.96         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GS 
       23.90        22.78        13.97         6.90        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       12.59        18.87        22.82        31.04        29.10        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92         2.14         6.97         3.72         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 
        8.98        96.69        59.01        28.96         1.74         2.43 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        9.11        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       18.810                        23.425 
[1] "0.1 - 149.6 (18.8)" "0.0 - 191.8 (23.4)"
[1] "hr=" "2.2"
D59V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                        28
  DEL PEAK  8(4P16.3) WILD-TYPE                                     352
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  8(4P16.3) MUTATED                               5
  DEL PEAK  8(4P16.3) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                  48
  DEL PEAK  8(4P16.3) WILD-TYPE                                56
D59V3, multiclass
                                         clus
vv                                        DEL PEAK  8(4P16.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          28
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                48
                                         clus
vv                                        DEL PEAK  8(4P16.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           352
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D59V4, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    19  62
  DEL PEAK  8(4P16.3) WILD-TYPE 119 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     19   62
  DEL PEAK  8(4P16.3) WILD-TYPE  119  305
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  NO                           19                           119
  YES                          62                           305
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4P16.3) MUTATED    58   4   4   4
  DEL PEAK  8(4P16.3) WILD-TYPE 293  18  13  26
D59V5, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  R0                          58                           293
  R1                           4                            18
  R2                           4                            13
  RX                           4                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4P16.3) MUTATED                                  1     1
  DEL PEAK  8(4P16.3) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(4P16.3) MUTATED                          14
  DEL PEAK  8(4P16.3) WILD-TYPE                        76
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4P16.3) MUTATED                                           3    57
  DEL PEAK  8(4P16.3) WILD-TYPE                                         6   300
D59V6, multiclass
                                           clus
vv                                          DEL PEAK  8(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              57
                                           clus
vv                                          DEL PEAK  8(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  WHITE                                                               300
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED     3  61
  DEL PEAK  8(4P16.3) WILD-TYPE  10 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      3   61
  DEL PEAK  8(4P16.3) WILD-TYPE   10  289
                        clus
vv                       DEL PEAK  8(4P16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK  8(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           289
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK  9(4P15.2) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P15.2) MUTATED    67  16
  DEL PEAK  9(4P15.2) WILD-TYPE 376  44
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           83                           420 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           16                            44 
$`DEL PEAK  9(4P15.2) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 
      149.56        60.53        36.82        19.96        91.04        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF 
        7.33        14.96         0.39         0.49         1.64         1.35 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H 
        0.76        16.87         1.71         5.95        57.80        45.53 
TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW 
        3.39        33.40        18.25         0.56        53.92        37.78 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       20.28        12.43        76.83        11.08         4.77        30.12 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-B5-A0JX 
       19.36         2.96         0.23        20.52         0.03        44.71 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD 
       17.85        75.72        36.82        11.87         5.03        34.13 
TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       34.95        36.49        12.56         6.81        10.22        24.13 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S 
       61.87        67.20        49.55        39.48        37.32        18.67 
TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
        1.41         6.77         0.72        35.38        12.39        91.96 
TCGA-EO-A1Y7 TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       18.81        34.39        27.16        22.26        16.34         4.54 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON 
       19.27        18.84        17.62         3.62        14.40        13.45 
TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2EX TCGA-FI-A2F8 
       45.76        27.35        13.84         6.44         9.07        25.02 
TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       41.06        13.15        10.82        23.97         7.00 

$`DEL PEAK  9(4P15.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        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-A1OK 
       15.95         7.92        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
       46.32         5.33         5.16         1.18         1.08         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        2.24         1.68        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        0.92        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.87         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
       21.99        23.31        86.07         8.22        39.42        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        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        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        33.73        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       16.96        13.55        15.25        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       68.71        33.40        40.50        26.33        17.75        27.32 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13        38.70         0.10         0.33         0.13         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.40        14.70        11.70        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        33.11        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
        7.92        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F 
        6.21        10.16        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        23.47        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 
       88.34        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        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       23.93        22.55         1.74         4.44        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-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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        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        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        32.38        19.40        19.36        35.15        12.89 
TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       26.96         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
        6.48        19.33        12.59        18.87        22.82        31.04 
TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       29.10        17.92         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01        28.93        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A914 
       26.01        45.01         1.74         2.43         9.11        12.92 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                        18.67                         23.47 
[1] "0.0 - 149.6 (18.7)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.2"
D60V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  9(4P15.2) MUTATED                                        29
  DEL PEAK  9(4P15.2) WILD-TYPE                                     351
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK  9(4P15.2) MUTATED                               5
  DEL PEAK  9(4P15.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  9(4P15.2) MUTATED                                  49
  DEL PEAK  9(4P15.2) WILD-TYPE                                55
D60V3, multiclass
                                         clus
vv                                        DEL PEAK  9(4P15.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          29
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                49
                                         clus
vv                                        DEL PEAK  9(4P15.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           351
  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"
D60V4, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED    18  65
  DEL PEAK  9(4P15.2) WILD-TYPE 120 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED     18   65
  DEL PEAK  9(4P15.2) WILD-TYPE  120  302
     clus
vv    DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  NO                           18                           120
  YES                          65                           302
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P15.2) MUTATED    54   4   5   6
  DEL PEAK  9(4P15.2) WILD-TYPE 297  18  12  24
D60V5, multiclass
    clus
vv   DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  R0                          54                           297
  R1                           4                            18
  R2                           5                            12
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4P15.2) MUTATED                                  1     1
  DEL PEAK  9(4P15.2) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(4P15.2) MUTATED                          18
  DEL PEAK  9(4P15.2) WILD-TYPE                        72
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(4P15.2) MUTATED                                           2    55
  DEL PEAK  9(4P15.2) WILD-TYPE                                         7   302
D60V6, multiclass
                                           clus
vv                                          DEL PEAK  9(4P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              55
                                           clus
vv                                          DEL PEAK  9(4P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               302
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED     4  59
  DEL PEAK  9(4P15.2) WILD-TYPE   9 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED      4   59
  DEL PEAK  9(4P15.2) WILD-TYPE    9  291
                        clus
vv                       DEL PEAK  9(4P15.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       DEL PEAK  9(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           291
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D61V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED    75  19
  DEL PEAK 10(4Q22.1) WILD-TYPE 368  41
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           94                           409 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           19                            41 
$`DEL PEAK 10(4Q22.1) MUTATED`
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        19.96        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        91.04        28.64         7.33         1.18         1.08 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AP-A052 
        0.85         0.49         1.64         1.35         0.76        21.99 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI 
       57.80        45.53        48.79       125.42         3.39        97.71 
TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       33.40        37.78        13.55        20.28        12.43        76.83 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
       11.08         4.77        30.12        61.18        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
       38.70         0.23        20.52         0.03         0.13         0.23 
TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
       80.38        75.72        36.82       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A0YV 
       12.79        33.11         5.03        34.13        36.49        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V 
        6.81        10.22        24.13        67.20        49.55        39.48 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A3DG 
       37.32        18.67         1.41         6.77        13.22         4.27 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A2CG TCGA-EO-A3AZ 
        4.11        35.38         9.37        91.96        32.38        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       26.96        22.26         4.54         6.90        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3QX 
       17.62        15.09         3.62        14.40        45.76        13.84 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
        5.88        34.98         9.07        28.93        25.02        41.06 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A914 TCGA-PG-A915 
        2.43        10.82        12.92         7.00 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        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-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.96         1.97         0.39        19.79         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         2.24         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.26         1.28         0.92        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        0.99         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        39.42        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        18.25        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        16.96        15.25 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        33.53        68.71        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       17.75        27.32        31.13         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.20         1.18         8.35        14.47         0.13        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        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         6.21        10.16        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 
       23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-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-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-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-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         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-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26        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        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        24.33        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        18.81        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        57.60        24.79        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       19.36        35.15        12.89        16.34         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       22.78        13.97        17.88        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33        12.59        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 
       13.45        31.04        29.10        27.35         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
        2.14         6.97         3.72         5.29        40.01        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       36.00         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A6IB 
       28.96        26.01        45.01         1.74        13.15         9.11 
TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       23.97        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       19.315                        23.340 
[1] "0.0 - 149.6 (19.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.2"
D61V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                        28
  DEL PEAK 10(4Q22.1) WILD-TYPE                                     352
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 10(4Q22.1) MUTATED                               6
  DEL PEAK 10(4Q22.1) WILD-TYPE                            15
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                  60
  DEL PEAK 10(4Q22.1) WILD-TYPE                                44
D61V3, multiclass
                                         clus
vv                                        DEL PEAK 10(4Q22.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          28
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                60
                                         clus
vv                                        DEL PEAK 10(4Q22.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           352
  MIXED SEROUS AND ENDOMETRIOID                                      15
  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"
D61V4, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    21  73
  DEL PEAK 10(4Q22.1) WILD-TYPE 117 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     21   73
  DEL PEAK 10(4Q22.1) WILD-TYPE  117  294
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                           21                           117
  YES                          73                           294
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED    58   6   7   6
  DEL PEAK 10(4Q22.1) WILD-TYPE 293  16  10  24
D61V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                          58                           293
  R1                           6                            16
  R2                           7                            10
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q22.1) MUTATED                                  0     3
  DEL PEAK 10(4Q22.1) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(4Q22.1) MUTATED                          24
  DEL PEAK 10(4Q22.1) WILD-TYPE                        66
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(4Q22.1) MUTATED                                           3    60
  DEL PEAK 10(4Q22.1) WILD-TYPE                                         6   297
D61V6, multiclass
                                           clus
vv                                          DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              60
                                           clus
vv                                          DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  WHITE                                                               297
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     3  63
  DEL PEAK 10(4Q22.1) WILD-TYPE  10 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      3   63
  DEL PEAK 10(4Q22.1) WILD-TYPE   10  287
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          63
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           287
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 11(4Q34.3) MUTATION ANALYSIS
D62V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q34.3) MUTATED   100  20
  DEL PEAK 11(4Q34.3) WILD-TYPE 343  40
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          120                           383 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                           20                            40 
$`DEL PEAK 11(4Q34.3) MUTATED`
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        19.96        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        91.04        28.64         7.33         1.18         1.08 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
        0.85         0.49         1.64         0.92         0.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 
        1.71         0.99        21.99        57.80        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX 
      125.42         3.39        97.71        33.40        41.95        33.73 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR 
        0.56        37.78        13.55        20.28        12.43        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2IO TCGA-AX-A3FS 
        4.77        30.12        61.18        19.36        38.70         0.23 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 
       20.52         0.03         0.13         0.13        80.38        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
        4.11        75.72        36.82       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 
       12.79        33.11         5.03        34.13        34.95        36.49 
TCGA-BG-A0YV TCGA-BG-A222 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD 
       12.56         9.57         6.81        10.22        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        67.20        49.55        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         1.41         6.77        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         4.11 
TCGA-DI-A0WH TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A22R TCGA-EO-A2CG 
       16.31        35.38        91.96        48.36        31.96        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       19.40        34.39        27.16        26.96        22.26        16.34 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A212 
        6.90        19.27        18.84        17.62        15.09         3.62 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A54A 
       14.40        45.76        29.10        27.35        13.84         3.72 
TCGA-EY-A72D TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
        5.88         9.07        28.93        25.02        41.06        45.01 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
        1.74         2.43        10.82        23.97        12.92         7.00 

$`DEL PEAK 11(4Q34.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        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-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.96         1.97         0.39        19.79         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         2.24         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
        1.94        15.95         1.87         2.33         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       63.16        36.36        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        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-AX-A05S 
       30.90        10.42        27.85        16.24        18.25        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        16.96        15.25 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39        71.24        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FT 
       26.33        17.75        27.32         2.96        31.13         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.33         0.13         0.20         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        17.88        13.74        17.10        11.01         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       62.14        41.06        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98         7.92        38.37        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       30.81        21.17        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       16.34        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-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        1.81        35.67        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-A56F 
       34.98         6.21        10.16        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        23.47        85.55        78.21 
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        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-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-A1NX TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.25        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A1BU 
       41.42         8.48        44.88         0.26        27.16        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30         9.37        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        24.33        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        18.81        37.71        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       27.12        57.60        24.79        19.36        35.15        12.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ 
       23.34        23.34        23.90        22.78        13.97        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A4KR 
       12.59        18.87        22.82        13.45        31.04         6.44 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92         2.14         6.97         5.29        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-PG-A6IB TCGA-PG-A916 
       59.01        28.96        26.01        13.15         9.11        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                       19.315                        23.470 
[1] "0.0 - 149.6 (19.3)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.8"
D62V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 11(4Q34.3) MUTATED                                        41
  DEL PEAK 11(4Q34.3) WILD-TYPE                                     339
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 11(4Q34.3) MUTATED                               8
  DEL PEAK 11(4Q34.3) WILD-TYPE                            13
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 11(4Q34.3) MUTATED                                  71
  DEL PEAK 11(4Q34.3) WILD-TYPE                                33
D62V3, multiclass
                                         clus
vv                                        DEL PEAK 11(4Q34.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          41
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                71
                                         clus
vv                                        DEL PEAK 11(4Q34.3) 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"
D62V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q34.3) MUTATED    27  93
  DEL PEAK 11(4Q34.3) WILD-TYPE 111 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q34.3) MUTATED     27   93
  DEL PEAK 11(4Q34.3) WILD-TYPE  111  274
     clus
vv    DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE
  NO                           27                           111
  YES                          93                           274
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q34.3) MUTATED    78   6   8   6
  DEL PEAK 11(4Q34.3) WILD-TYPE 273  16   9  24
D62V5, multiclass
    clus
vv   DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE
  R0                          78                           273
  R1                           6                            16
  R2                           8                             9
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q34.3) MUTATED                                  0     4
  DEL PEAK 11(4Q34.3) WILD-TYPE                                4    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(4Q34.3) MUTATED                          34
  DEL PEAK 11(4Q34.3) WILD-TYPE                        56
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(4Q34.3) MUTATED                                           3    71
  DEL PEAK 11(4Q34.3) WILD-TYPE                                         6   286
D62V6, multiclass
                                           clus
vv                                          DEL PEAK 11(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                          34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              71
                                           clus
vv                                          DEL PEAK 11(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            56
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  WHITE                                                               286
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q34.3) MUTATED     3  81
  DEL PEAK 11(4Q34.3) WILD-TYPE  10 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q34.3) MUTATED      3   81
  DEL PEAK 11(4Q34.3) WILD-TYPE   10  269
                        clus
vv                       DEL PEAK 11(4Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       DEL PEAK 11(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           269
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 12(5Q12.1) MUTATION ANALYSIS
D63V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q12.1) MUTATED    83  17
  DEL PEAK 12(5Q12.1) WILD-TYPE 360  43
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          100                           403 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           17                            43 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
      149.56        65.75        19.96        17.59        11.44        36.33 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD 
        7.33        14.96         1.18         0.39         0.85         0.49 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS 
        1.64        22.26         0.92         1.35         0.76        16.87 
TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI 
        1.71        45.53        48.79       125.42         3.39        97.71 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C8 
       33.40        18.25        33.73        53.92        37.78        13.55 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HF TCGA-AX-A3FX 
       20.28        76.83         4.77        30.12        19.36         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 
        0.20        20.52         0.13         0.13        80.38        17.85 
TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD 
       75.72        50.89        12.79        33.11         5.03        34.13 
TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC 
       34.95         7.92        36.49        12.56         6.81        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V 
       10.16        24.13        16.64        67.20        49.55        39.48 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NX 
       11.51        31.07        18.67         6.77        13.22        18.25 
TCGA-D1-A1O0 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
        2.07         9.37        31.10        91.96        48.36        24.33 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ 
       10.92        18.81        37.71        32.38        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       26.96        22.26        23.90        19.27        18.84        17.62 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A3QX TCGA-EY-A547 TCGA-FI-A2D2 
        8.55         3.62        14.40        13.84        17.92        36.00 
TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       96.69        28.93        25.02        41.06        45.01        13.15 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A914 TCGA-PG-A915 
        2.43        10.82        12.92         7.00 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95         7.92         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       28.64         5.33         5.16         1.08         1.97        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40         3.02         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49         1.28        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.94        15.95         1.87         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       19.20        16.96        15.25        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H5 
       54.12        67.50        25.12        36.39        11.08        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       33.53        61.18        68.71        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.10         0.33         0.03         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB 
       23.01        17.88        13.74        17.10        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        14.40        14.70        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC 
       15.29       116.25        96.30        78.81        62.14        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        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
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         6.21 
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-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         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-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-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
       22.92         1.41         0.72        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26         4.27         4.11        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        35.38        12.39        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R 
        2.37         6.67        16.01         7.36        16.80        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        24.79        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       19.36        35.15        12.89        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT 
       22.78        13.97         6.90        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       12.43        15.81         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        13.45        45.76        31.04        29.10        27.35 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
        6.44         2.14         6.97         3.72         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A6IB 
       59.01         9.07        28.96        26.01         1.74         9.11 
TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       23.97        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                        18.74                         23.47 
[1] "0.1 - 149.6 (18.7)" "0.0 - 191.8 (23.5)"
[1] "hr=" "1.8"
D63V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                        32
  DEL PEAK 12(5Q12.1) WILD-TYPE                                     348
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 12(5Q12.1) MUTATED                               4
  DEL PEAK 12(5Q12.1) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                  65
  DEL PEAK 12(5Q12.1) WILD-TYPE                                39
D63V3, multiclass
                                         clus
vv                                        DEL PEAK 12(5Q12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          32
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                65
                                         clus
vv                                        DEL PEAK 12(5Q12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           348
  MIXED SEROUS AND ENDOMETRIOID                                      17
  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"
D63V4, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    24  77
  DEL PEAK 12(5Q12.1) WILD-TYPE 114 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     24   77
  DEL PEAK 12(5Q12.1) WILD-TYPE  114  290
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                           24                           114
  YES                          77                           290
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED    65   4   4   8
  DEL PEAK 12(5Q12.1) WILD-TYPE 286  18  13  22
D63V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                          65                           286
  R1                           4                            18
  R2                           4                            13
  RX                           8                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(5Q12.1) MUTATED                                  0     3
  DEL PEAK 12(5Q12.1) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(5Q12.1) MUTATED                          26
  DEL PEAK 12(5Q12.1) WILD-TYPE                        64
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(5Q12.1) MUTATED                                           3    60
  DEL PEAK 12(5Q12.1) WILD-TYPE                                         6   297
D63V6, multiclass
                                           clus
vv                                          DEL PEAK 12(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              60
                                           clus
vv                                          DEL PEAK 12(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  WHITE                                                               297
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     5  70
  DEL PEAK 12(5Q12.1) WILD-TYPE   8 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      5   70
  DEL PEAK 12(5Q12.1) WILD-TYPE    8  280
                        clus
vv                       DEL PEAK 12(5Q12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       DEL PEAK 12(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           280
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D64V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED    35   8
  DEL PEAK 13(6Q26) WILD-TYPE 408  52
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         43                         460 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                          8                          52 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-AJ-A23N TCGA-AJ-A2QM 
      149.56        60.53        19.96        36.33         1.08         0.85 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05J TCGA-AP-A0L9 
        1.12         1.64         0.76        16.87        36.89       125.42 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H8 
        0.56        37.78        16.96        25.12         4.77        61.18 
TCGA-AX-A2IO TCGA-AX-A3G3 TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-BG-A0YV 
       38.70         0.03        36.82        50.89        11.87        12.56 
TCGA-BG-A3PP TCGA-BS-A0V6 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A3DG 
        6.81        62.79        22.55        11.51        29.92         4.27 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A3AS 
       91.96        48.36        24.33        37.71        57.60        34.39 
TCGA-EO-A3B1 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-H5-A2HR 
       26.96        29.10         6.44        36.00        41.06         1.74 
TCGA-PG-A7D5 
       23.97 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       14.96         1.18         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
        3.02         0.49         0.76         2.24         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
        1.35        15.62         1.94        15.95         1.87         1.71 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        2.33         0.99         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       45.53         7.86        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ 
      110.37         3.39        63.16        36.36        97.71        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        18.25        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       67.50        36.39        11.08        30.12        71.24        33.53 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32         2.96        31.13         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.13         0.20        20.52         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 
       14.40        14.70        11.70        15.29        12.79       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98         7.92        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        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         6.21        10.22        10.16 
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        23.47        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 
       67.20        88.34        85.84        82.39        81.57        72.72 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ 
       73.25        59.51        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       28.67        23.93         1.74         4.44        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-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        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         1.41         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         6.77         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-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48        44.88         0.26         4.11        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-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       31.10        23.38        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        18.81        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       33.01        27.12        24.79        32.38        19.40        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       35.15        12.89        27.16        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 
       15.81         8.55         6.48        19.33        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       27.35        13.84        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        5.29         5.88        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84         8.98        96.69        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.96        25.02        26.01        45.01        13.15         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       10.82         9.11        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.03                        0.10 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     149.56                      191.84 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     25.120                      22.375 
[1] "0.0 - 149.6 (25.1)" "0.1 - 191.8 (22.4)"
[1] "hr=" "1.5"
D64V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                        12
  DEL PEAK 13(6Q26) WILD-TYPE                                     368
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 13(6Q26) MUTATED                               3
  DEL PEAK 13(6Q26) WILD-TYPE                            18
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                  28
  DEL PEAK 13(6Q26) WILD-TYPE                                76
D64V3, multiclass
                                         clus
vv                                        DEL PEAK 13(6Q26) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        12
  MIXED SEROUS AND ENDOMETRIOID                                   3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              28
                                         clus
vv                                        DEL PEAK 13(6Q26) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         368
  MIXED SEROUS AND ENDOMETRIOID                                    18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    10  33
  DEL PEAK 13(6Q26) WILD-TYPE 128 334
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     10   33
  DEL PEAK 13(6Q26) WILD-TYPE  128  334
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                         10                         128
  YES                        33                         334
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(6Q26) MUTATED    33   1   1   2
  DEL PEAK 13(6Q26) WILD-TYPE 318  21  16  28
D64V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  R0                        33                         318
  R1                         1                          21
  R2                         1                          16
  RX                         2                          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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q26) MUTATED                                  0     2
  DEL PEAK 13(6Q26) WILD-TYPE                                4    17
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(6Q26) MUTATED                           9
  DEL PEAK 13(6Q26) WILD-TYPE                        81
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(6Q26) MUTATED                                           0    27
  DEL PEAK 13(6Q26) WILD-TYPE                                         9   330
D64V6, multiclass
                                           clus
vv                                          DEL PEAK 13(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             2
  BLACK OR AFRICAN AMERICAN                                         9
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         0
  WHITE                                                            27
                                           clus
vv                                          DEL PEAK 13(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    4
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                          81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           9
  WHITE                                                             330
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED     0  29
  DEL PEAK 13(6Q26) WILD-TYPE  13 321
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      0   29
  DEL PEAK 13(6Q26) WILD-TYPE   13  321
                        clus
vv                       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             0                          13
  NOT HISPANIC OR LATINO                        29                         321
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 14(7P22.3) MUTATION ANALYSIS
D65V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7P22.3) MUTATED    51  15
  DEL PEAK 14(7P22.3) WILD-TYPE 392  45
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           66                           437 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           15                            45 
$`DEL PEAK 14(7P22.3) MUTATED`
TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3EJ TCGA-AJ-A3QS 
       19.96        36.33        14.96         1.18         1.64        16.87 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF 
        5.95        23.31        45.53        36.89        48.79         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW 
       97.71        41.95        18.25         0.56        53.92        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HJ 
       16.96        20.28        11.08         4.77        30.12        27.32 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        2.96        38.70        23.01        17.85         4.11        75.72 
TCGA-B5-A1N2 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZP 
       12.79         6.81        10.22        16.64        67.20        29.95 
TCGA-D1-A16V TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
        1.41         0.72        44.88        35.38         9.37        91.96 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       48.36        24.33        16.01        37.71        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ 
       34.39        22.26         3.62        14.40        45.76        29.10 
TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       34.98        59.01         9.07        28.93        25.02        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A915 
       41.06        45.01         1.74         2.43        10.82         7.00 

$`DEL PEAK 14(7P22.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        9.60         8.02        91.04        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.85         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        2.24         1.68        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87         1.71         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 
        2.70         0.13        83.67        21.99        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       39.42        57.80         7.86        12.20        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        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        33.73        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.55        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       17.75        31.13         0.23         0.10         0.33         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.03         0.13         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       11.01         8.71       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 
       45.90        43.96        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        11.87        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        33.11         5.03        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       13.78        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        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         6.21        10.16        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        23.47 
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        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ 
       49.55        63.16        66.48        16.83        19.79         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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-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-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 
        6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42         8.48         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        17.06         2.37         6.67 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        18.81        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       33.01        27.12        57.60        24.79        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33        12.59        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        31.04        27.35        13.84         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
        2.14         6.97         3.72         5.29         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       33.99        36.00         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-K6-A3WQ TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
       28.96        13.15         9.11        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                         0.56                          0.03 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                        97.71                        191.84 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                       22.635                        22.820 
[1] "0.6 - 97.7 (22.6)"  "0.0 - 191.8 (22.8)"
[1] "hr=" "2.4"
D65V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 14(7P22.3) MUTATED                                        21
  DEL PEAK 14(7P22.3) WILD-TYPE                                     359
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 14(7P22.3) MUTATED                               5
  DEL PEAK 14(7P22.3) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 14(7P22.3) MUTATED                                  41
  DEL PEAK 14(7P22.3) WILD-TYPE                                63
D65V3, multiclass
                                         clus
vv                                        DEL PEAK 14(7P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          21
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                41
                                         clus
vv                                        DEL PEAK 14(7P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           359
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D65V4, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED    14  53
  DEL PEAK 14(7P22.3) WILD-TYPE 124 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED     14   53
  DEL PEAK 14(7P22.3) WILD-TYPE  124  314
     clus
vv    DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  NO                           14                           124
  YES                          53                           314
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(7P22.3) MUTATED    45   4   4   6
  DEL PEAK 14(7P22.3) WILD-TYPE 306  18  13  24
D65V5, multiclass
    clus
vv   DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  R0                          45                           306
  R1                           4                            18
  R2                           4                            13
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(7P22.3) MUTATED                                  0     2
  DEL PEAK 14(7P22.3) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(7P22.3) MUTATED                          20
  DEL PEAK 14(7P22.3) WILD-TYPE                        70
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(7P22.3) MUTATED                                           1    39
  DEL PEAK 14(7P22.3) WILD-TYPE                                         8   318
D65V6, multiclass
                                           clus
vv                                          DEL PEAK 14(7P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              39
                                           clus
vv                                          DEL PEAK 14(7P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     2  44
  DEL PEAK 14(7P22.3) WILD-TYPE  11 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      2   44
  DEL PEAK 14(7P22.3) WILD-TYPE   11  306
                        clus
vv                       DEL PEAK 14(7P22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 14(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           306
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 15(7Q11.22) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(7Q11.22) MUTATED    35   4
  DEL PEAK 15(7Q11.22) WILD-TYPE 408  56
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            39                            464 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                             4                             56 
$`DEL PEAK 15(7Q11.22) MUTATED`
TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AJ-A3TW 
       19.96        36.33        91.04         0.49         0.76         1.71 
TCGA-AP-A05H TCGA-AP-A0LF TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2HK TCGA-AX-A2IO 
       45.53         3.39        20.28        11.08         2.96        38.70 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-B5-A11I TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
       80.38         4.11        75.72         6.81        10.22        10.16 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G7 
       16.64        67.20        39.48        18.67         2.07        44.88 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EY-A1GC 
        4.11        35.38        48.36        19.40        22.26         4.54 
TCGA-EY-A212 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A547 TCGA-FI-A2EU TCGA-FI-A2EW 
        3.62        45.76        29.10        17.92        96.69        59.01 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       26.01        41.06        45.01 

$`DEL PEAK 15(7Q11.22) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        7.33        14.96         1.18         1.08         1.97         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         0.85         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        2.24         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87        16.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        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 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        18.25        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        27.32        31.13         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.23         1.18         8.35        14.47         0.13        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
        5.03        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        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 
        6.21        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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-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         1.41         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         6.77         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-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48         0.26         4.27        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        91.96 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        24.33        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        57.60        24.79        32.38 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        19.36        35.15        12.89        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81         8.55         6.48        19.33        12.59 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 
       14.40        18.87        22.82        13.45        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84         6.44         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98         9.07        28.93        28.96        25.02 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        1.74        13.15         2.43        10.82         9.11        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                          0.49                           0.03 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                         96.69                         191.84 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                        20.280                         22.965 
[1] "0.5 - 96.7 (20.3)"  "0.0 - 191.8 (23.0)"
[1] "hr=" "1.2"
D66V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 15(7Q11.22) MUTATED                                        13
  DEL PEAK 15(7Q11.22) WILD-TYPE                                     367
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 15(7Q11.22) MUTATED                               2
  DEL PEAK 15(7Q11.22) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 15(7Q11.22) MUTATED                                  24
  DEL PEAK 15(7Q11.22) WILD-TYPE                                80
D66V3, multiclass
                                         clus
vv                                        DEL PEAK 15(7Q11.22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           13
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 24
                                         clus
vv                                        DEL PEAK 15(7Q11.22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            367
  MIXED SEROUS AND ENDOMETRIOID                                       19
  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"
D66V4, binary
                                cls
clus                               0   1
  DEL PEAK 15(7Q11.22) MUTATED     8  31
  DEL PEAK 15(7Q11.22) WILD-TYPE 130 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(7Q11.22) MUTATED      8   31
  DEL PEAK 15(7Q11.22) WILD-TYPE  130  336
     clus
vv    DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE
  NO                             8                            130
  YES                           31                            336
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 15(7Q11.22) MUTATED    29   3   2   2
  DEL PEAK 15(7Q11.22) WILD-TYPE 322  19  15  28
D66V5, multiclass
    clus
vv   DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE
  R0                           29                            322
  R1                            3                             19
  R2                            2                             15
  RX                            2                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(7Q11.22) MUTATED                                  0     0
  DEL PEAK 15(7Q11.22) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(7Q11.22) MUTATED                          10
  DEL PEAK 15(7Q11.22) WILD-TYPE                        80
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 15(7Q11.22) MUTATED                                           1
  DEL PEAK 15(7Q11.22) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK 15(7Q11.22) MUTATED      24
  DEL PEAK 15(7Q11.22) WILD-TYPE   333
D66V6, multiclass
                                           clus
vv                                          DEL PEAK 15(7Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               24
                                           clus
vv                                          DEL PEAK 15(7Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                333
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(7Q11.22) MUTATED     1  27
  DEL PEAK 15(7Q11.22) WILD-TYPE  12 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(7Q11.22) MUTATED      1   27
  DEL PEAK 15(7Q11.22) WILD-TYPE   12  323
                        clus
vv                       DEL PEAK 15(7Q11.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       DEL PEAK 15(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            323
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 16(7Q31.1) MUTATION ANALYSIS
D67V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(7Q31.1) MUTATED    42  10
  DEL PEAK 16(7Q31.1) WILD-TYPE 401  50
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           52                           451 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           10                            50 
$`DEL PEAK 16(7Q31.1) MUTATED`
TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       19.96        36.33        91.04         1.18         1.08         0.49 
TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CR 
        0.76        57.80        41.95        37.78        20.28        11.08 
TCGA-AX-A2HK TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A1MY TCGA-BG-A0M6 TCGA-BG-A0YV 
        2.96        80.38        75.72        11.87         7.92        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A0ZZ 
        6.81        10.22        10.16        24.13        67.20        22.55 
TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 
       39.48        18.67        13.22        18.25         2.07        44.88 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CH TCGA-EO-A3B1 
        4.11        35.38        91.96        48.36        19.40        26.96 
TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A4KR 
       22.26         4.54         3.62        13.45        45.76         6.44 
TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        3.72        96.69        59.01        26.01        41.06        45.01 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       10.82        23.97        12.92         7.00 

$`DEL PEAK 16(7Q31.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 
       28.27        20.81        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         7.92        11.44 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        7.33        14.96         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40         3.02         1.12         0.76         2.24         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.64        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65         1.35        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.87        16.87         1.71         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       18.25        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39         4.77        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.13         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47         0.13        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84       102.31 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.40        14.70        11.70        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 
      116.25        96.30        78.81        62.14        33.11         5.03 
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-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        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         6.21        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        23.47 
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        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         1.41         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         6.77 
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-A1NY 
       24.30         2.33        22.92         1.41         0.72        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48         0.26         4.27        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30         9.37        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        24.33        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        18.81        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       33.01        27.12        57.60        24.79        32.38        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        35.15        12.89        27.16        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.90        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       17.88        17.62        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
        8.55         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       22.82        31.04        29.10        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        2.14         6.97         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX 
       33.99        36.00         7.99        13.84         8.98         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.93        28.96        25.02         1.74        13.15         2.43 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        9.11        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                         0.49                          0.03 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                        96.69                        191.84 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                        19.68                         23.31 
[1] "0.5 - 96.7 (19.7)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "1.9"
D67V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 16(7Q31.1) MUTATED                                         9
  DEL PEAK 16(7Q31.1) WILD-TYPE                                     371
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 16(7Q31.1) MUTATED                               3
  DEL PEAK 16(7Q31.1) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 16(7Q31.1) MUTATED                                  40
  DEL PEAK 16(7Q31.1) WILD-TYPE                                64
D67V3, multiclass
                                         clus
vv                                        DEL PEAK 16(7Q31.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           9
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                40
                                         clus
vv                                        DEL PEAK 16(7Q31.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           371
  MIXED SEROUS AND ENDOMETRIOID                                      18
  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"
D67V4, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED    13  39
  DEL PEAK 16(7Q31.1) WILD-TYPE 125 328
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED     13   39
  DEL PEAK 16(7Q31.1) WILD-TYPE  125  328
     clus
vv    DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  NO                           13                           125
  YES                          39                           328
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(7Q31.1) MUTATED    37   2   3   5
  DEL PEAK 16(7Q31.1) WILD-TYPE 314  20  14  25
D67V5, multiclass
    clus
vv   DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  R0                          37                           314
  R1                           2                            20
  R2                           3                            14
  RX                           5                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(7Q31.1) MUTATED                                  0     0
  DEL PEAK 16(7Q31.1) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(7Q31.1) MUTATED                          15
  DEL PEAK 16(7Q31.1) WILD-TYPE                        75
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 16(7Q31.1) MUTATED                                           1    31
  DEL PEAK 16(7Q31.1) WILD-TYPE                                         8   326
D67V6, multiclass
                                           clus
vv                                          DEL PEAK 16(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              31
                                           clus
vv                                          DEL PEAK 16(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED     1  37
  DEL PEAK 16(7Q31.1) WILD-TYPE  12 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED      1   37
  DEL PEAK 16(7Q31.1) WILD-TYPE   12  313
                        clus
vv                       DEL PEAK 16(7Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       DEL PEAK 16(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           313
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 17(7Q36.1) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q36.1) MUTATED    48  13
  DEL PEAK 17(7Q36.1) WILD-TYPE 395  47
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           61                           442 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           13                            47 
$`DEL PEAK 17(7Q36.1) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-AJ-A23M 
       37.02        19.96        11.44        36.33        91.04         1.18 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A0L9 
        1.08         0.49         0.76         5.95        57.80       125.42 
TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A1DQ TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1CA 
        3.39        36.36        41.95        28.54        16.96        20.28 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A1MY 
       11.08         4.77         2.96        80.38        75.72        11.87 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A221 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
        7.92        12.56         1.81         6.81        10.22        10.16 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A1NU 
       24.13        67.20        22.55        39.48        18.67        13.22 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO 
       18.25         2.07        44.88         4.11        35.38         9.37 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU 
       91.96        48.36        32.38        19.40        26.96        22.26 
TCGA-EY-A1GC TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A4KR TCGA-FI-A2EU 
        4.54         3.62        13.45        45.76         6.44        96.69 
TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-PG-A5BC TCGA-PG-A7D5 
       59.01        26.01        41.06        45.01        10.82        23.97 
TCGA-PG-A915 
        7.00 

$`DEL PEAK 17(7Q36.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        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-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
       46.32        28.64         5.33         5.16         7.33        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       22.49        22.26         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
        1.71         2.33         0.99         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H 
       21.99        23.31        86.07         8.22        39.42        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89         7.86        12.20        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        63.16        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       18.25        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        13.55        15.25        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.13        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       11.01         4.11         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        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       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        33.11         5.03        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-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
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-A220 TCGA-BG-A222 
       14.73        14.01        15.45        15.45        14.27         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
        6.21        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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        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         1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42         8.48         0.26         4.27 
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-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       31.10        23.38        17.06         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.01         7.36        16.80        10.92        18.81        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KW 
       34.39        19.36        35.15        12.89        27.16        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       15.81         8.55         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        31.04        29.10        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92         2.14         6.97         3.72         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR 
        8.98         9.07        28.93        28.96        25.02         1.74 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 
       13.15         2.43         9.11        12.92        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                         0.49                          0.03 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                       19.400                        23.325 
[1] "0.5 - 125.4 (19.4)" "0.0 - 191.8 (23.3)"
[1] "hr=" "2.2"
D68V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 17(7Q36.1) MUTATED                                        12
  DEL PEAK 17(7Q36.1) WILD-TYPE                                     368
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 17(7Q36.1) MUTATED                               4
  DEL PEAK 17(7Q36.1) WILD-TYPE                            17
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 17(7Q36.1) MUTATED                                  45
  DEL PEAK 17(7Q36.1) WILD-TYPE                                59
D68V3, multiclass
                                         clus
vv                                        DEL PEAK 17(7Q36.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          12
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                45
                                         clus
vv                                        DEL PEAK 17(7Q36.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           368
  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"
D68V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED    17  44
  DEL PEAK 17(7Q36.1) WILD-TYPE 121 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED     17   44
  DEL PEAK 17(7Q36.1) WILD-TYPE  121  323
     clus
vv    DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  NO                           17                           121
  YES                          44                           323
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(7Q36.1) MUTATED    43   2   4   6
  DEL PEAK 17(7Q36.1) WILD-TYPE 308  20  13  24
D68V5, multiclass
    clus
vv   DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  R0                          43                           308
  R1                           2                            20
  R2                           4                            13
  RX                           6                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q36.1) MUTATED                                  0     2
  DEL PEAK 17(7Q36.1) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(7Q36.1) MUTATED                          17
  DEL PEAK 17(7Q36.1) WILD-TYPE                        73
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(7Q36.1) MUTATED                                           1    36
  DEL PEAK 17(7Q36.1) WILD-TYPE                                         8   321
D68V6, multiclass
                                           clus
vv                                          DEL PEAK 17(7Q36.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              36
                                           clus
vv                                          DEL PEAK 17(7Q36.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED     1  44
  DEL PEAK 17(7Q36.1) WILD-TYPE  12 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED      1   44
  DEL PEAK 17(7Q36.1) WILD-TYPE   12  306
                        clus
vv                       DEL PEAK 17(7Q36.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 17(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           306
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D69V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED    84  21
  DEL PEAK 18(8P23.2) WILD-TYPE 359  39
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          105                           398 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           21                            39 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M 
       65.75        11.44        36.33        46.32        28.64         1.18 
TCGA-AJ-A23N TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05D 
        1.08         0.92         1.35        16.87         1.71        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI 
       45.53        36.89        48.79       125.42         3.39        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA 
       41.95        18.25         0.56        37.78        16.96        20.28 
TCGA-AX-A1CC TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       12.43        25.12        36.39         4.77        30.12        71.24 
TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A3FX TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI 
       19.36        17.75         0.13         0.03         0.13         0.13 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MR 
       80.38        23.01        17.85         4.11        75.72       191.84 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
      102.31        11.87        12.79         5.03        34.13        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0YU TCGA-BG-A2AE TCGA-BG-A3PP 
        7.92        36.49        21.17        14.83        23.70         6.81 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ 
       10.16        24.13        61.87        67.20        29.95        22.55 
TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A1NU 
       39.48        27.42        11.51        18.67         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
        0.72        44.88         4.11        35.38         9.37        12.39 
TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ 
       91.96        18.81        57.60        32.38        34.39        27.16 
TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 
       22.26        23.90        15.09        15.81         3.62        14.40 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
        3.72         5.88        36.00        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC 
       28.93        41.06        45.01         1.74        13.15        10.82 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       23.97        12.92         7.00 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
        8.02        91.04         5.33         5.16         7.33        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        0.49         1.12         0.76         2.24         1.68         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         1.28        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW 
       15.62         0.76         1.94        15.95         1.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        39.42         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       20.91       117.99       110.37        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24        33.73        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF 
       13.28        19.20        13.55        15.25        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2H8 
       72.56        54.12        67.50        11.08        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       68.71        33.40        40.50        26.33        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        38.70         0.23         0.10         0.33         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
       20.52         0.23         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       15.29       116.25        96.30        78.81        62.14        33.11 
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 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        30.81        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       52.83        56.58        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        35.67 
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         6.21        10.22 
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        23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-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-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-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
        1.05         3.95         3.52        41.42         8.48         0.26 
TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       24.33        16.01         7.36        16.80        10.92        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CH 
       31.96        35.05        33.01        27.12        24.79        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        35.15        12.89        26.96        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        22.78        13.97         6.90        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX 
       17.88        17.62        16.11        12.43         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
       19.33        12.59        18.87        22.82        45.76        31.04 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
        2.14         6.97         5.29        40.01        34.98        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        7.99        13.84         8.98        28.96        25.02        26.01 
TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        2.43         9.11        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       191.84                        185.79 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        19.36                         23.34 
[1] "0.0 - 191.8 (19.4)" "0.1 - 185.8 (23.3)"
[1] "hr=" "2.2"
D69V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                        31
  DEL PEAK 18(8P23.2) WILD-TYPE                                     349
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 18(8P23.2) MUTATED                               5
  DEL PEAK 18(8P23.2) WILD-TYPE                            16
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                  70
  DEL PEAK 18(8P23.2) WILD-TYPE                                34
D69V3, multiclass
                                         clus
vv                                        DEL PEAK 18(8P23.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          31
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                70
                                         clus
vv                                        DEL PEAK 18(8P23.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           349
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    24  82
  DEL PEAK 18(8P23.2) WILD-TYPE 114 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     24   82
  DEL PEAK 18(8P23.2) WILD-TYPE  114  285
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                           24                           114
  YES                          82                           285
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED    64   5   7  10
  DEL PEAK 18(8P23.2) WILD-TYPE 287  17  10  20
D69V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                          64                           287
  R1                           5                            17
  R2                           7                            10
  RX                          10                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(8P23.2) MUTATED                                  1     2
  DEL PEAK 18(8P23.2) WILD-TYPE                                3    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(8P23.2) MUTATED                          31
  DEL PEAK 18(8P23.2) WILD-TYPE                        59
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(8P23.2) MUTATED                                           2    64
  DEL PEAK 18(8P23.2) WILD-TYPE                                         7   293
D69V6, multiclass
                                           clus
vv                                          DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              64
                                           clus
vv                                          DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            59
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               293
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     1  75
  DEL PEAK 18(8P23.2) WILD-TYPE  12 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      1   75
  DEL PEAK 18(8P23.2) WILD-TYPE   12  275
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          75
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           275
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 19(8P21.2) MUTATION ANALYSIS
D70V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(8P21.2) MUTATED    84  20
  DEL PEAK 19(8P21.2) WILD-TYPE 359  40
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          104                           399 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                           20                            40 
$`DEL PEAK 19(8P21.2) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       65.75        11.44        36.33        91.04        46.32        28.64 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
        1.18         1.08         0.92         1.35        16.87         1.71 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       57.80        45.53        36.89        48.79       125.42         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 
       97.71        41.95        18.25         0.56        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       13.55        20.28        12.43        25.12        36.39         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI 
       30.12        71.24        19.36         0.03         0.13         0.13 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MR 
       80.38        23.01        17.85         4.11        75.72       191.84 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
      102.31        11.87        12.79         5.03        34.13        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 
        7.92        36.49        21.17        23.70         6.81        10.16 
TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V 
       24.13        61.87        67.20        29.95        22.55        39.48 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
       27.42        11.51        18.67         6.77        13.22         0.72 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y8 
       44.88         4.11        35.38        12.39        91.96        37.71 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       57.60        32.38        34.39        27.16        26.96        22.26 
TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON 
       23.90        15.09        15.81         3.62        14.40        13.45 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A72D 
       29.10        27.35        13.84         6.44        17.92         5.88 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       34.98        36.00        96.69        59.01         9.07        28.93 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 
       41.06        45.01         1.74        13.15        10.82        23.97 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`DEL PEAK 19(8P21.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92         9.60 
TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O 
        8.02         5.33         5.16         7.33        14.96         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76         2.24         1.68         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         1.28        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU 
        0.76         1.94        15.95         1.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        39.42         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        33.73        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        28.54        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       19.20        15.25        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       67.50        11.08        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       40.50        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
       20.52         0.23         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       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        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
       17.36        16.57        50.89        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       15.29       116.25        96.30        78.81        62.14        33.11 
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 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        30.81        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.01        15.45        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       35.67        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        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        23.47        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        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         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-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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30         9.37        31.10        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        24.33        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        18.81        31.96        35.05        33.01        27.12 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW 
       24.79        19.40        19.36        35.15        12.89        16.34 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.34        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW 
       18.84        17.88        17.62        16.11        12.43         8.55 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
        6.48        19.33        12.59        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       31.04         2.14         6.97         3.72         5.29        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 
       33.99         7.99        13.84         8.98        28.96        25.02 
TCGA-FI-A2F9 TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       26.01         2.43         9.11        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                       191.84                        185.79 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                        22.78                         22.82 
[1] "0.0 - 191.8 (22.8)" "0.1 - 185.8 (22.8)"
[1] "hr=" "1.9"
D70V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 19(8P21.2) MUTATED                                        23
  DEL PEAK 19(8P21.2) WILD-TYPE                                     357
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 19(8P21.2) MUTATED                               6
  DEL PEAK 19(8P21.2) WILD-TYPE                            15
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 19(8P21.2) MUTATED                                  75
  DEL PEAK 19(8P21.2) WILD-TYPE                                29
D70V3, multiclass
                                         clus
vv                                        DEL PEAK 19(8P21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          23
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                75
                                         clus
vv                                        DEL PEAK 19(8P21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           357
  MIXED SEROUS AND ENDOMETRIOID                                      15
  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"
D70V4, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P21.2) MUTATED    24  80
  DEL PEAK 19(8P21.2) WILD-TYPE 114 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P21.2) MUTATED     24   80
  DEL PEAK 19(8P21.2) WILD-TYPE  114  287
     clus
vv    DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE
  NO                           24                           114
  YES                          80                           287
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P21.2) MUTATED    65   5   7   8
  DEL PEAK 19(8P21.2) WILD-TYPE 286  17  10  22
D70V5, multiclass
    clus
vv   DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE
  R0                          65                           286
  R1                           5                            17
  R2                           7                            10
  RX                           8                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P21.2) MUTATED                                  1     2
  DEL PEAK 19(8P21.2) WILD-TYPE                                3    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(8P21.2) MUTATED                          30
  DEL PEAK 19(8P21.2) WILD-TYPE                        60
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(8P21.2) MUTATED                                           2    62
  DEL PEAK 19(8P21.2) WILD-TYPE                                         7   295
D70V6, multiclass
                                           clus
vv                                          DEL PEAK 19(8P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              62
                                           clus
vv                                          DEL PEAK 19(8P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            60
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               295
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P21.2) MUTATED     2  71
  DEL PEAK 19(8P21.2) WILD-TYPE  11 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P21.2) MUTATED      2   71
  DEL PEAK 19(8P21.2) WILD-TYPE   11  279
                        clus
vv                       DEL PEAK 19(8P21.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       DEL PEAK 19(8P21.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           279
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 20(9P23) MUTATION ANALYSIS
D71V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(9P23) MUTATED    58  11
  DEL PEAK 20(9P23) WILD-TYPE 385  49
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         69                         434 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         11                          49 
$`DEL PEAK 20(9P23) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP 
      149.56        87.32        36.82        19.96        17.59        42.35 
TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD 
       36.33        28.64         7.33         1.18         1.08         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH 
        1.12         2.24         1.64         1.28         0.92         0.76 
TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
        0.99        45.53        48.79        97.71        41.95        18.25 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A2H2 
        0.56        37.78        16.96        13.55        76.83         4.77 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MS 
        0.13         0.13        17.85         4.11        36.82       102.31 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A139 
      116.25        33.11        34.95        36.49        15.45        10.16 
TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S 
       16.64        49.55        22.55        39.48        37.32        18.67 
TCGA-D1-A1O0 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y7 
        2.07        35.38        12.39        91.96        24.33        18.81 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A214 
       32.38        27.16        26.96        19.27        15.09        14.40 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
        6.44         3.72         5.88        36.00         9.07        28.93 
TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 
       13.15        10.82        23.97 

$`DEL PEAK 20(9P23) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM 
        3.22       105.37        74.10        57.53        65.75        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF 
       68.65        19.59        24.62        29.06        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 
       11.44         9.60         8.02        91.04        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16        14.96         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40         3.02         0.76         1.68        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         1.35        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.95         1.87        16.87         1.71         2.33         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       20.91       125.42       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        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 
       30.90        10.42        27.85        16.24        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        28.54        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA 
       40.11        65.88        13.28        19.20        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08        30.12        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       27.32         2.96        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.33         0.20        20.52         0.03         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         8.71       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        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        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       191.84        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        11.87        15.29        12.79        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14         5.03        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        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        23.47        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 
       67.20        88.34        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        62.79        63.58        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26         4.27         4.11        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        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         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        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        24.79        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       12.89        22.26        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       22.78        13.97         6.90        18.84        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       31.04        29.10        27.35        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        6.97         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69        59.01        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A6IB 
       26.01        41.06        45.01         1.74         2.43         9.11 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                       0.13                        0.03 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                     149.56                      191.84 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                     18.670                      23.325 
[1] "0.1 - 149.6 (18.7)" "0.0 - 191.8 (23.3)"
[1] "hr=" "1.6"
D71V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 20(9P23) MUTATED                                        27
  DEL PEAK 20(9P23) WILD-TYPE                                     353
                             vv
clus                          MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 20(9P23) MUTATED                               4
  DEL PEAK 20(9P23) WILD-TYPE                            17
                             vv
clus                          SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 20(9P23) MUTATED                                  39
  DEL PEAK 20(9P23) WILD-TYPE                                65
D71V3, multiclass
                                         clus
vv                                        DEL PEAK 20(9P23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        27
  MIXED SEROUS AND ENDOMETRIOID                                   4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              39
                                         clus
vv                                        DEL PEAK 20(9P23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         353
  MIXED SEROUS AND ENDOMETRIOID                                    17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                             cls
clus                            0   1
  DEL PEAK 20(9P23) MUTATED    13  57
  DEL PEAK 20(9P23) WILD-TYPE 125 310
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(9P23) MUTATED     13   57
  DEL PEAK 20(9P23) WILD-TYPE  125  310
     clus
vv    DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  NO                         13                         125
  YES                        57                         310
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(9P23) MUTATED    45   3   5   5
  DEL PEAK 20(9P23) WILD-TYPE 306  19  12  25
D71V5, multiclass
    clus
vv   DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  R0                        45                         306
  R1                         3                          19
  R2                         5                          12
  RX                         5                          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"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(9P23) MUTATED                                  1     2
  DEL PEAK 20(9P23) WILD-TYPE                                3    17
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(9P23) MUTATED                          18
  DEL PEAK 20(9P23) WILD-TYPE                        72
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(9P23) MUTATED                                           2    43
  DEL PEAK 20(9P23) WILD-TYPE                                         7   314
D71V6, multiclass
                                           clus
vv                                          DEL PEAK 20(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             2
  BLACK OR AFRICAN AMERICAN                                        18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            43
                                           clus
vv                                          DEL PEAK 20(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              17
  BLACK OR AFRICAN AMERICAN                                          72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             314
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(9P23) MUTATED     1  50
  DEL PEAK 20(9P23) WILD-TYPE  12 300
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(9P23) MUTATED      1   50
  DEL PEAK 20(9P23) WILD-TYPE   12  300
                        clus
vv                       DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  HISPANIC OR LATINO                             1                          12
  NOT HISPANIC OR LATINO                        50                         300
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 21(9Q21.2) MUTATION ANALYSIS
D72V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(9Q21.2) MUTATED    93  23
  DEL PEAK 21(9Q21.2) WILD-TYPE 350  37
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          116                           387 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                           23                            37 
$`DEL PEAK 21(9Q21.2) MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OH 
       87.32        36.82        19.96        17.59        42.35        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QN 
       91.04        28.64         7.33         1.18         0.39         2.40 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.49         1.12         2.24         1.64        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 
        0.92         0.76         1.71         0.99        21.99         5.95 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ 
       57.80        45.53        48.79       125.42        97.71        41.95 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF 
       18.25        33.73        53.92        37.78        16.96        76.83 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
       36.39        11.08        30.12        61.18        19.36         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         0.13        20.52         0.13         0.13        80.38 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU 
       17.85         4.11        75.72        36.82       102.31        50.89 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE 
       11.87        12.79       116.25        33.11         5.03        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC 
        7.92        36.49        12.56        15.45         1.81        10.22 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZQ 
       10.16        24.13        16.64        61.87        49.55         8.55 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       22.55        39.48        37.32        31.07        18.67         1.41 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DI-A1NN 
       28.08        13.22         0.72         2.07         4.11        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y7 
        9.37        12.39        91.96        48.36        24.33        18.81 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW 
       37.71        32.38        19.40        27.16        26.96        16.34 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
        4.54        19.27        15.81         8.55        12.59         3.62 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY 
       14.40        13.45        29.10         6.44        17.92        34.98 
TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ 
       36.00        28.93        25.02        41.06        45.01        13.15 
TCGA-PG-A5BC TCGA-PG-A914 
       10.82        12.92 

$`DEL PEAK 21(9Q21.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78         3.22       105.37        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ 
       23.21        68.65        19.59        24.62        29.06        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
        7.92        11.44         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16        14.96         1.08         1.97        19.79         0.85 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        3.02         0.76         1.68        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         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       16.87         2.33         2.70         0.13        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
       86.07         8.22        39.42        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
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        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        28.54        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        19.20        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H2 
       20.05        72.56        54.12        67.50        25.12         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        33.53        68.71        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW 
       17.75        27.32        31.13        38.70         0.10         0.33 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.03         0.23         1.18         8.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       17.88        13.74        17.10        11.01         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC 
       11.70        15.29        96.30        78.81        62.14        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 
       34.98        38.37        28.27        10.72        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       23.47        43.30        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       14.01        15.45        14.27         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
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-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ 
       23.47        85.55        78.21         4.80        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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
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         6.77         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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ 
       41.42         8.48        44.88         0.26         4.27        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LX 
       16.31        39.29        36.62        24.30        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU 
       24.79        34.39        19.36        35.15        12.89        22.26 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97         6.90        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       17.88        17.62        15.09        16.11        12.43         6.48 
TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       19.33        18.87        22.82        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       13.84         2.14         6.97         3.72         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        33.99         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 
       59.01         9.07        28.96        26.01         1.74         2.43 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        23.97         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                        19.04                         23.47 
[1] "0.1 - 125.4 (19.0)" "0.0 - 191.8 (23.5)"
[1] "hr=" "2.3"
D72V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 21(9Q21.2) MUTATED                                        46
  DEL PEAK 21(9Q21.2) WILD-TYPE                                     334
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 21(9Q21.2) MUTATED                              10
  DEL PEAK 21(9Q21.2) WILD-TYPE                            11
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 21(9Q21.2) MUTATED                                  61
  DEL PEAK 21(9Q21.2) WILD-TYPE                                43
D72V3, multiclass
                                         clus
vv                                        DEL PEAK 21(9Q21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          46
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                61
                                         clus
vv                                        DEL PEAK 21(9Q21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           334
  MIXED SEROUS AND ENDOMETRIOID                                      11
  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"
D72V4, binary
                               cls
clus                              0   1
  DEL PEAK 21(9Q21.2) MUTATED    27  90
  DEL PEAK 21(9Q21.2) WILD-TYPE 111 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9Q21.2) MUTATED     27   90
  DEL PEAK 21(9Q21.2) WILD-TYPE  111  277
     clus
vv    DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE
  NO                           27                           111
  YES                          90                           277
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(9Q21.2) MUTATED    74   5   7   9
  DEL PEAK 21(9Q21.2) WILD-TYPE 277  17  10  21
D72V5, multiclass
    clus
vv   DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE
  R0                          74                           277
  R1                           5                            17
  R2                           7                            10
  RX                           9                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(9Q21.2) MUTATED                                  1     1
  DEL PEAK 21(9Q21.2) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(9Q21.2) MUTATED                          29
  DEL PEAK 21(9Q21.2) WILD-TYPE                        61
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(9Q21.2) MUTATED                                           2    77
  DEL PEAK 21(9Q21.2) WILD-TYPE                                         7   280
D72V6, multiclass
                                           clus
vv                                          DEL PEAK 21(9Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              77
                                           clus
vv                                          DEL PEAK 21(9Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               280
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(9Q21.2) MUTATED     4  79
  DEL PEAK 21(9Q21.2) WILD-TYPE   9 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9Q21.2) MUTATED      4   79
  DEL PEAK 21(9Q21.2) WILD-TYPE    9  271
                        clus
vv                       DEL PEAK 21(9Q21.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          79
                        clus
vv                       DEL PEAK 21(9Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           271
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 22(9Q34.2) MUTATION ANALYSIS
D73V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9Q34.2) MUTATED    96  22
  DEL PEAK 22(9Q34.2) WILD-TYPE 347  38
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          118                           385 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                           22                            38 
$`DEL PEAK 22(9Q34.2) MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0VP 
       87.32        65.75        36.82        19.96        17.59        42.35 
TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A2QK 
       11.44        91.04        28.64         7.33         1.18         0.39 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.49         1.12         2.24         1.64        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05H 
        0.92         0.76         0.99        21.99         5.95        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        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CP 
        0.56        53.92        37.78        16.96        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3FS TCGA-AX-A3FX 
       11.08        30.12        61.18        19.36         0.23         0.13 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 
       20.52         0.13         0.13        80.38        23.01        17.85 
TCGA-B5-A0KB TCGA-B5-A11H TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
        4.11        88.34        36.82       102.31        50.89        11.87 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
      116.25        33.11         5.03        34.13        34.95         7.92 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A139 
       36.49        12.56        15.45         1.81        10.22        10.16 
TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ 
       24.13        61.87        67.20        49.55         8.55        22.55 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K 
       39.48        37.32        31.07        18.67         1.41        28.08 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN 
       13.22         0.72         2.07        44.88         4.11        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 
        9.37        31.10        91.96        48.36        24.33        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 
       18.81        37.71        32.38        19.40        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GV 
       16.34         4.54        23.90         6.90        17.62        15.81 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A4KR 
        8.55         3.62        14.40        13.45        29.10         6.44 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       34.98        36.00         9.07        28.93        25.02        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A5BC 
       41.06        45.01        13.15        10.82 

$`DEL PEAK 22(9Q34.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
       32.78         3.22       105.37        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF 
       68.65        19.59        24.62        29.06        15.95         7.92 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33         9.60         8.02        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.96         1.08         1.97        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        3.02         0.76         1.68        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         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87         1.71         2.33         2.70         0.13        83.67 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N 
       23.31        86.07         8.22        39.42        57.80         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
        6.71        30.90        10.42        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        13.28        19.20        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        71.24        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.10         0.33         0.20         0.03         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       25.91        17.88        13.74        17.10        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N 
      185.79       113.36        75.72        54.44        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29        12.79        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       62.14        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        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
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-A220 TCGA-BG-A222 TCGA-BG-A2AD 
       14.73        14.01        15.45        14.27         9.57        35.67 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
        6.21        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        23.47        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        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16O 
       37.51        36.79        27.42        11.51        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-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         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-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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ 
        3.52        41.42         8.48         0.26         4.27        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX 
       16.31        39.29        36.62        24.30        12.39        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       17.06         2.37         6.67        16.01         7.36        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EY-A1G7 
       34.39        19.36        35.15        12.89        22.26         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       22.78        13.97        19.27        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       16.11        12.43         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       22.82        45.76        31.04        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
        2.14         6.97         3.72         5.29         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       28.96         1.74         2.43         9.11        23.97        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                       21.255                        23.310 
[1] "0.1 - 125.4 (21.3)" "0.0 - 191.8 (23.3)"
[1] "hr=" "2"  
D73V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 22(9Q34.2) MUTATED                                        49
  DEL PEAK 22(9Q34.2) WILD-TYPE                                     331
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 22(9Q34.2) MUTATED                              10
  DEL PEAK 22(9Q34.2) WILD-TYPE                            11
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 22(9Q34.2) MUTATED                                  60
  DEL PEAK 22(9Q34.2) WILD-TYPE                                44
D73V3, multiclass
                                         clus
vv                                        DEL PEAK 22(9Q34.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          49
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                60
                                         clus
vv                                        DEL PEAK 22(9Q34.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           331
  MIXED SEROUS AND ENDOMETRIOID                                      11
  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"
D73V4, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.2) MUTATED    26  93
  DEL PEAK 22(9Q34.2) WILD-TYPE 112 274
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.2) MUTATED     26   93
  DEL PEAK 22(9Q34.2) WILD-TYPE  112  274
     clus
vv    DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE
  NO                           26                           112
  YES                          93                           274
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9Q34.2) MUTATED    74   5   6  11
  DEL PEAK 22(9Q34.2) WILD-TYPE 277  17  11  19
D73V5, multiclass
    clus
vv   DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE
  R0                          74                           277
  R1                           5                            17
  R2                           6                            11
  RX                          11                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9Q34.2) MUTATED                                  0     2
  DEL PEAK 22(9Q34.2) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(9Q34.2) MUTATED                          28
  DEL PEAK 22(9Q34.2) WILD-TYPE                        62
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(9Q34.2) MUTATED                                           3    78
  DEL PEAK 22(9Q34.2) WILD-TYPE                                         6   279
D73V6, multiclass
                                           clus
vv                                          DEL PEAK 22(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              78
                                           clus
vv                                          DEL PEAK 22(9Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            62
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  WHITE                                                               279
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.2) MUTATED     3  83
  DEL PEAK 22(9Q34.2) WILD-TYPE  10 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.2) MUTATED      3   83
  DEL PEAK 22(9Q34.2) WILD-TYPE   10  267
                        clus
vv                       DEL PEAK 22(9Q34.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK 22(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           267
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 23(10Q23.31) MUTATION ANALYSIS
D74V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 23(10Q23.31) MUTATED    56  11
  DEL PEAK 23(10Q23.31) WILD-TYPE 387  49
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             67                             436 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             11                              49 
$`DEL PEAK 23(10Q23.31) MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A2QM 
       87.32        65.75        11.44        36.33        14.96         0.85 
TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A0L9 
        1.12        22.26         0.92         1.71        21.99       125.42 
TCGA-AP-A0LF TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1CR TCGA-AX-A2HK 
        3.39        33.73         0.56        53.92        11.08         2.96 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K2 
       20.52         0.03         0.13         0.13        80.38        25.91 
TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A1MS TCGA-B5-A3FD TCGA-BG-A0M8 TCGA-BG-A18C 
       23.01         4.11       102.31        33.11        36.49        15.45 
TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-D1-A160 TCGA-D1-A16I TCGA-D1-A16J 
        6.81         4.80        67.20         3.68        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG 
       31.07        28.01        28.08        13.22         2.07         4.27 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A2CH 
        4.11        35.38        91.96        10.92        32.38        19.40 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM 
       34.39        27.16        26.96        16.34        23.90         6.90 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A4KR 
       17.62        15.09         8.55        14.40        27.35         6.44 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 
       36.00        96.69        25.02        41.06        13.15         2.43 
TCGA-PG-A914 
       12.92 

$`DEL PEAK 23(10Q23.31) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
       32.78         3.22       105.37        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       91.04        46.32        28.64         5.33         5.16         7.33 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        1.18         1.08         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        3.02         0.49         0.76         2.24         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49         1.28        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62         0.76         1.94        15.95         1.87        16.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
        2.33         0.99         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       23.31        86.07         8.22        39.42        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89         7.86        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24        18.25        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39         4.77        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        27.32        31.13        38.70         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.33         0.13         0.20         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K4 
       44.71        32.55        28.64        28.34        30.51        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        17.85        11.01         8.71       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 
       12.79       116.25        96.30        78.81        62.14         5.03 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        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         6.21        10.22        10.16 
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-A0TG 
        9.86        46.95        23.47        85.55        78.21        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        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        21.99        39.48 
TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08        29.88         1.91        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       27.42        33.63        10.65         0.69        18.67         1.41 
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 
        6.77         1.58         7.00         0.99        30.44         1.28 
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-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30         9.37        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        24.33        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        18.81        37.71        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       33.01        27.12        57.60        24.79        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       12.89        22.26         6.21        14.99         4.54         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL 
       24.36        27.16        23.34        23.34        22.78        13.97 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59         3.62        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 
       13.45        45.76        31.04        29.10        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
        2.14         6.97         3.72         5.29         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       34.98        33.99         7.99        13.84         8.98        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
        9.07        28.93        28.96        26.01        45.01         1.74 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       10.82         9.11        23.97         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                         125.42                          191.84 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                          17.62                           23.34 
[1] "0.0 - 125.4 (17.6)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.8"
D74V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 23(10Q23.31) MUTATED                                        29
  DEL PEAK 23(10Q23.31) WILD-TYPE                                     351
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 23(10Q23.31) MUTATED                               5
  DEL PEAK 23(10Q23.31) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 23(10Q23.31) MUTATED                                  34
  DEL PEAK 23(10Q23.31) WILD-TYPE                                70
D74V3, multiclass
                                         clus
vv                                        DEL PEAK 23(10Q23.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            29
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  34
                                         clus
vv                                        DEL PEAK 23(10Q23.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             351
  MIXED SEROUS AND ENDOMETRIOID                                        16
  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"
D74V4, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10Q23.31) MUTATED    10  58
  DEL PEAK 23(10Q23.31) WILD-TYPE 128 309
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q23.31) MUTATED     10   58
  DEL PEAK 23(10Q23.31) WILD-TYPE  128  309
     clus
vv    DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  NO                             10                             128
  YES                            58                             309
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 23(10Q23.31) MUTATED    42   2   5   6
  DEL PEAK 23(10Q23.31) WILD-TYPE 309  20  12  24
D74V5, multiclass
    clus
vv   DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  R0                            42                             309
  R1                             2                              20
  R2                             5                              12
  RX                             6                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10Q23.31) MUTATED                                  0     3
  DEL PEAK 23(10Q23.31) WILD-TYPE                                4    16
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(10Q23.31) MUTATED                          16
  DEL PEAK 23(10Q23.31) WILD-TYPE                        74
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 23(10Q23.31) MUTATED                                           2
  DEL PEAK 23(10Q23.31) WILD-TYPE                                         7
                                 vv
clus                              WHITE
  DEL PEAK 23(10Q23.31) MUTATED      40
  DEL PEAK 23(10Q23.31) WILD-TYPE   317
D74V6, multiclass
                                           clus
vv                                          DEL PEAK 23(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                                40
                                           clus
vv                                          DEL PEAK 23(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  16
  BLACK OR AFRICAN AMERICAN                                              74
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               7
  WHITE                                                                 317
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10Q23.31) MUTATED     2  46
  DEL PEAK 23(10Q23.31) WILD-TYPE  11 304
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q23.31) MUTATED      2   46
  DEL PEAK 23(10Q23.31) WILD-TYPE   11  304
                        clus
vv                       DEL PEAK 23(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            46
                        clus
vv                       DEL PEAK 23(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             304
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 24(11P15.5) MUTATION ANALYSIS
D75V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(11P15.5) MUTATED    76  17
  DEL PEAK 24(11P15.5) WILD-TYPE 367  43
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            93                            410 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            17                             43 
$`DEL PEAK 24(11P15.5) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
      149.56        65.75        60.53        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A3BD 
       46.32        28.64        14.96         1.18         0.39         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF 
        1.12         2.24         1.64        22.26         0.92         1.35 
TCGA-AJ-A3NH TCGA-AP-A05A TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
        0.76        39.42         3.39        97.71        41.95        18.25 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 
       37.78        16.96        20.28        76.83        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI 
       30.12         0.33        20.52         0.03         0.13         0.13 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 
       80.38        17.85         4.11        36.82       102.31        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0MC TCGA-BG-A0YV 
      116.25        33.11        34.13        34.95        41.52        12.56 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-D1-A15V TCGA-D1-A169 
       10.22        10.16        16.64        61.87        39.48        37.32 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 
       11.51        18.67        28.08         0.72        18.25         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
        4.27         4.11         9.37        12.39        31.10        91.96 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       48.36        24.33        37.71        32.38        19.40        34.39 
TCGA-EO-A3B1 TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A212 
       26.96        23.90        19.27        18.84        15.09         3.62 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW 
       14.40        45.76        29.10         3.72        36.00        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
        9.07        28.93        41.06         1.74        13.15         2.43 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
       10.82        23.97         7.00 

$`DEL PEAK 24(11P15.5) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       68.65        19.96        17.59        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K5 
       42.35        15.95         7.92         9.60         8.02         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16         7.33         1.08         1.97        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40         3.02         0.76         1.68        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
        1.28        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
        1.87        16.87         1.71         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        57.80        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       20.91        48.79       125.42       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        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-AW-A1PO 
       30.90        10.42        27.85        16.24        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        19.20        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       25.12        36.39        71.24        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       33.40        40.50        19.36        26.33        17.75        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX 
        2.96        31.13        38.70         0.23         0.10         0.13 
TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.20         0.23         1.18         8.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        11.87        15.29        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14         5.03        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       28.27        10.72        48.56        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B 
       11.31         6.81        35.90        34.98         6.21        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 
       23.47        85.55        78.21         4.80        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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74         4.44        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-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-A16V TCGA-D1-A16X 
       31.07        33.63        10.65         0.69         1.41         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         6.77 
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-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41        13.22        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       44.88         0.26        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        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
       16.01         7.36        16.80        10.92        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       35.05        33.01        27.12        57.60        24.79        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       35.15        12.89        27.16        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR 
       23.34        22.78        13.97         6.90        17.88        17.62 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 
       12.59        18.87        22.82        13.45        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       13.84         6.44        17.92         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        34.98        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
        8.98        96.69        28.96        25.02        26.01        45.01 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        9.11        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                        149.56                         191.84 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                         18.84                          23.34 
[1] "0.0 - 149.6 (18.8)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.9"
D75V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 24(11P15.5) MUTATED                                        32
  DEL PEAK 24(11P15.5) WILD-TYPE                                     348
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 24(11P15.5) MUTATED                               5
  DEL PEAK 24(11P15.5) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 24(11P15.5) MUTATED                                  57
  DEL PEAK 24(11P15.5) WILD-TYPE                                47
D75V3, multiclass
                                         clus
vv                                        DEL PEAK 24(11P15.5) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           32
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 57
                                         clus
vv                                        DEL PEAK 24(11P15.5) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            348
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                                cls
clus                               0   1
  DEL PEAK 24(11P15.5) MUTATED    16  78
  DEL PEAK 24(11P15.5) WILD-TYPE 122 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11P15.5) MUTATED     16   78
  DEL PEAK 24(11P15.5) WILD-TYPE  122  289
     clus
vv    DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  NO                            16                            122
  YES                           78                            289
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(11P15.5) MUTATED    59   3   7   6
  DEL PEAK 24(11P15.5) WILD-TYPE 292  19  10  24
D75V5, multiclass
    clus
vv   DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  R0                           59                            292
  R1                            3                             19
  R2                            7                             10
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(11P15.5) MUTATED                                  1     3
  DEL PEAK 24(11P15.5) WILD-TYPE                                3    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(11P15.5) MUTATED                          26
  DEL PEAK 24(11P15.5) WILD-TYPE                        64
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 24(11P15.5) MUTATED                                           1
  DEL PEAK 24(11P15.5) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK 24(11P15.5) MUTATED      59
  DEL PEAK 24(11P15.5) WILD-TYPE   298
D75V6, multiclass
                                           clus
vv                                          DEL PEAK 24(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                           26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               59
                                           clus
vv                                          DEL PEAK 24(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                298
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(11P15.5) MUTATED     4  67
  DEL PEAK 24(11P15.5) WILD-TYPE   9 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11P15.5) MUTATED      4   67
  DEL PEAK 24(11P15.5) WILD-TYPE    9  283
                        clus
vv                       DEL PEAK 24(11P15.5) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 24(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            283
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 25(11Q14.1) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(11Q14.1) MUTATED    52  11
  DEL PEAK 25(11Q14.1) WILD-TYPE 391  49
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            63                            440 
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            11                             49 
$`DEL PEAK 25(11Q14.1) MUTATED`
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K3 
       60.53        36.82        19.96        11.44        91.04        46.32 
TCGA-A5-A2K4 TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       28.64         0.39         0.85         0.49         2.24         1.64 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A0LF TCGA-AP-A3K1 
        1.35         0.76        16.87         1.71         3.39        18.25 
TCGA-AX-A1C7 TCGA-AX-A1CR TCGA-AX-A2IO TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P 
       16.96        11.08        38.70        23.01        17.85        36.82 
TCGA-B5-A11Q TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0YV 
       32.09       116.25        33.11        34.13         7.92        12.56 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
        6.81        10.22        24.13        22.55        37.32        11.51 
TCGA-D1-A16S TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A8L9 
       18.67         4.27        35.38         9.37        12.39        24.33 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP 
       37.71        32.38        22.26        23.90        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A3L3 
       17.62        15.09         8.55        12.59        45.76        27.35 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX 
        6.44         3.72         5.88        36.00        96.69         9.07 
TCGA-FI-A2EY TCGA-KJ-A3U4 TCGA-PG-A915 
       28.93         2.43         7.00 

$`DEL PEAK 25(11Q14.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        38.37        28.27        20.81 
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-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
        1.97        19.79         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68        14.66        22.49        22.26         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        2.33         0.99         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89         7.86        12.20        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        63.16        36.36        97.71 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        41.95        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        33.73         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D 
       35.34        45.99        66.58        34.98        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU 
       51.09        27.39        30.02        60.66        35.01        28.54 
TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       37.78        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       13.55        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       40.50        19.36        26.33        17.75        27.32         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.03         0.13         0.23         1.18         8.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.13        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S 
       54.44        45.90        43.96        40.50        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29        12.79        96.30        78.81        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        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         6.21        10.16        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 
       23.47        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        67.20        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        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-A16V 
       29.92        31.07        33.63        10.65         0.69         1.41 
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 
        6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.11        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30        31.10        91.96        23.38        48.36        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        2.37         6.67        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       18.81        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        26.96        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
        8.15        24.36        27.16        23.34        23.34        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       13.97         6.90        17.88        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33         3.62        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       13.45        31.04        29.10        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
        6.97         5.29        40.01        34.98        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       13.84         8.98        59.01        28.96        25.02        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB 
       41.06        45.01         1.74        13.15        10.82         9.11 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.97        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                          0.39                           0.03 
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                        116.25                         191.84 
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                         17.85                          23.47 
[1] "0.4 - 116.2 (17.9)" "0.0 - 191.8 (23.5)"
[1] "hr=" "2"  
D76V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 25(11Q14.1) MUTATED                                        20
  DEL PEAK 25(11Q14.1) WILD-TYPE                                     360
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 25(11Q14.1) MUTATED                               6
  DEL PEAK 25(11Q14.1) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 25(11Q14.1) MUTATED                                  38
  DEL PEAK 25(11Q14.1) WILD-TYPE                                66
D76V3, multiclass
                                         clus
vv                                        DEL PEAK 25(11Q14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           20
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        DEL PEAK 25(11Q14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            360
  MIXED SEROUS AND ENDOMETRIOID                                       15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(11Q14.1) MUTATED    12  52
  DEL PEAK 25(11Q14.1) WILD-TYPE 126 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(11Q14.1) MUTATED     12   52
  DEL PEAK 25(11Q14.1) WILD-TYPE  126  315
     clus
vv    DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE
  NO                            12                            126
  YES                           52                            315
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(11Q14.1) MUTATED    43   4   3   5
  DEL PEAK 25(11Q14.1) WILD-TYPE 308  18  14  25
D76V5, multiclass
    clus
vv   DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE
  R0                           43                            308
  R1                            4                             18
  R2                            3                             14
  RX                            5                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(11Q14.1) MUTATED                                  1     2
  DEL PEAK 25(11Q14.1) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(11Q14.1) MUTATED                          19
  DEL PEAK 25(11Q14.1) WILD-TYPE                        71
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 25(11Q14.1) MUTATED                                           0
  DEL PEAK 25(11Q14.1) WILD-TYPE                                         9
                                vv
clus                             WHITE
  DEL PEAK 25(11Q14.1) MUTATED      38
  DEL PEAK 25(11Q14.1) WILD-TYPE   319
D76V6, multiclass
                                           clus
vv                                          DEL PEAK 25(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               38
                                           clus
vv                                          DEL PEAK 25(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              9
  WHITE                                                                319
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(11Q14.1) MUTATED     5  47
  DEL PEAK 25(11Q14.1) WILD-TYPE   8 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(11Q14.1) MUTATED      5   47
  DEL PEAK 25(11Q14.1) WILD-TYPE    8  303
                        clus
vv                       DEL PEAK 25(11Q14.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 25(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            303
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 26(11Q25) MUTATION ANALYSIS
D77V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(11Q25) MUTATED    69  16
  DEL PEAK 26(11Q25) WILD-TYPE 374  44
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          85                          418 
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          16                           44 
$`DEL PEAK 26(11Q25) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 
       65.75        60.53        36.82        17.59        11.44        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       46.32        28.64         0.85         0.49         2.24         1.64 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05D 
        0.92         0.76        16.87         1.71        21.99        57.80 
TCGA-AP-A0LF TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A2H4 
        3.39        18.25        33.73        16.96        13.55        30.12 
TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 
       38.70         0.13         0.23         0.13        23.01        17.85 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
       36.82        32.09        50.89        12.79       116.25        33.11 
TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0YV TCGA-BG-A18C 
       34.13         7.92        36.49        41.52        12.56        15.45 
TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
        6.81        24.13        16.64        22.55        37.32        11.51 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       18.67         1.41         4.27        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A2CG 
       31.10        10.92        18.81        37.71        57.60        32.38 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP 
       22.26        16.34        23.90         6.90        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO 
       17.62        15.09         8.55        12.59        14.40        45.76 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2EU 
       27.35        13.84         6.44         3.72        40.01        96.69 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A914 
        9.07        28.93        25.02         1.74         2.43        12.92 
TCGA-PG-A915 
        7.00 

$`DEL PEAK 26(11Q25) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K5 
       15.95         7.92        36.33         9.60         8.02         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.16         7.33        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.39        19.79         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        1.68        14.66        22.49        22.26         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
        2.33         0.99         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        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        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       65.88        13.28        19.20        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       20.05        76.83        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39        11.08         4.77        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32         2.96        31.13         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.13         0.20        20.52         0.03         1.18         8.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB 
       25.91        17.88        13.74        17.10        11.01         4.11 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       185.79       113.36        88.34        75.72        54.44 
TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       45.90        43.96        40.50        33.50        27.35        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       191.84 
TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
      102.31        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       96.30        78.81        62.14         5.03        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        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       38.37        28.27        10.72        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        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         6.21        10.22        10.16 
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-A0TE TCGA-BS-A0TG TCGA-BS-A0TI 
       23.47        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        67.20        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        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-A16X 
       29.92        31.07        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-A179 
       17.49        19.53         6.64        30.15        18.02         6.77 
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-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
       24.33        16.01         7.36        16.80        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       33.01        27.12        24.79        19.40        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        27.16        26.96         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       22.78        13.97        17.88        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
        6.48        19.33         3.62        18.87        22.82        13.45 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       31.04        29.10        17.92         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        8.98        59.01        28.96        26.01        41.06        45.01 
TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 
       13.15        10.82         9.11        23.97        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                        0.13                         0.03 
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                      116.25                       191.84 
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                      17.620                       23.815 
[1] "0.1 - 116.2 (17.6)" "0.0 - 191.8 (23.8)"
[1] "hr=" "2.2"
D77V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 26(11Q25) MUTATED                                        31
  DEL PEAK 26(11Q25) WILD-TYPE                                     349
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 26(11Q25) MUTATED                               6
  DEL PEAK 26(11Q25) WILD-TYPE                            15
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 26(11Q25) MUTATED                                  49
  DEL PEAK 26(11Q25) WILD-TYPE                                55
D77V3, multiclass
                                         clus
vv                                        DEL PEAK 26(11Q25) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         31
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               49
                                         clus
vv                                        DEL PEAK 26(11Q25) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          349
  MIXED SEROUS AND ENDOMETRIOID                                     15
  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"
D77V4, binary
                              cls
clus                             0   1
  DEL PEAK 26(11Q25) MUTATED    13  73
  DEL PEAK 26(11Q25) WILD-TYPE 125 294
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(11Q25) MUTATED     13   73
  DEL PEAK 26(11Q25) WILD-TYPE  125  294
     clus
vv    DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE
  NO                          13                          125
  YES                         73                          294
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 26(11Q25) MUTATED    56   4   5   7
  DEL PEAK 26(11Q25) WILD-TYPE 295  18  12  23
D77V5, multiclass
    clus
vv   DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE
  R0                         56                          295
  R1                          4                           18
  R2                          5                           12
  RX                          7                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(11Q25) MUTATED                                  1     2
  DEL PEAK 26(11Q25) WILD-TYPE                                3    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(11Q25) MUTATED                          24
  DEL PEAK 26(11Q25) WILD-TYPE                        66
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 26(11Q25) MUTATED                                           1    51
  DEL PEAK 26(11Q25) WILD-TYPE                                         8   306
D77V6, multiclass
                                           clus
vv                                          DEL PEAK 26(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             51
                                           clus
vv                                          DEL PEAK 26(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            8
  WHITE                                                              306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(11Q25) MUTATED     3  61
  DEL PEAK 26(11Q25) WILD-TYPE  10 289
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(11Q25) MUTATED      3   61
  DEL PEAK 26(11Q25) WILD-TYPE   10  289
                        clus
vv                       DEL PEAK 26(11Q25) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         61
                        clus
vv                       DEL PEAK 26(11Q25) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          289
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 27(12Q23.1) MUTATION ANALYSIS
D78V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12Q23.1) MUTATED    36  10
  DEL PEAK 27(12Q23.1) WILD-TYPE 407  50
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            46                            457 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            10                             50 
$`DEL PEAK 27(12Q23.1) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A3IA 
       65.75        19.96        36.33        91.04        28.64         0.92 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LF TCGA-AP-A0LI 
        1.35         0.76        21.99        45.53         3.39        97.71 
TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A2H2 TCGA-B5-A0JN 
       33.40        18.25        33.73         0.56         4.77        80.38 
TCGA-B5-A0K3 TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BG-A18C 
       23.01        12.79        34.13        34.95        12.56        15.45 
TCGA-BK-A139 TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A3DH 
       10.16        24.13        22.55        39.48        18.67         4.11 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW 
       12.39        91.96        10.92        27.16        26.96        16.34 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EU 
        3.62        14.40        29.10         6.44         3.72        96.69 
TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A915 
       41.06        13.15        10.82         7.00 

$`DEL PEAK 27(12Q23.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       60.53        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       20.81        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         7.92        11.44         9.60 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP 
        8.02        46.32         5.33         5.16         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18         1.08         1.97         0.39        19.79         0.85 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40         3.02         0.49         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87         1.71         2.33         0.99         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      125.42       117.99       110.37        63.16        36.36        31.73 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       83.97        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.85        16.24        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       13.28        19.20        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       12.43        20.05        76.83        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08        30.12        71.24        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.10         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       13.74        17.10        17.85        11.01         4.11         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.87        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       33.11         5.03        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
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        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        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         1.41         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         6.77         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-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48        44.88         0.26         4.27        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38         9.37        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 
       23.38        48.36        17.06         2.37         6.67        24.33 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.01         7.36        16.80        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        57.60        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU 
       19.40        34.39        19.36        35.15        12.89        22.26 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
       19.27        18.84        17.88        17.62        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81         8.55         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        13.45        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       13.84        17.92         2.14         6.97         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        34.98        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A7D5 
       26.01        45.01         1.74         2.43         9.11        23.97 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       12.92        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                          0.56                           0.03 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                         97.71                         191.84 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                        19.315                         23.310 
[1] "0.6 - 97.7 (19.3)"  "0.0 - 191.8 (23.3)"
[1] "hr=" "2.3"
D78V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 27(12Q23.1) MUTATED                                        11
  DEL PEAK 27(12Q23.1) WILD-TYPE                                     369
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 27(12Q23.1) MUTATED                               3
  DEL PEAK 27(12Q23.1) WILD-TYPE                            18
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 27(12Q23.1) MUTATED                                  32
  DEL PEAK 27(12Q23.1) WILD-TYPE                                72
D78V3, multiclass
                                         clus
vv                                        DEL PEAK 27(12Q23.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           11
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 32
                                         clus
vv                                        DEL PEAK 27(12Q23.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            369
  MIXED SEROUS AND ENDOMETRIOID                                       18
  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"
D78V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(12Q23.1) MUTATED     8  38
  DEL PEAK 27(12Q23.1) WILD-TYPE 130 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12Q23.1) MUTATED      8   38
  DEL PEAK 27(12Q23.1) WILD-TYPE  130  329
     clus
vv    DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE
  NO                             8                            130
  YES                           38                            329
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12Q23.1) MUTATED    28   1   4   6
  DEL PEAK 27(12Q23.1) WILD-TYPE 323  21  13  24
D78V5, multiclass
    clus
vv   DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE
  R0                           28                            323
  R1                            1                             21
  R2                            4                             13
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(12Q23.1) MUTATED                                  1     0
  DEL PEAK 27(12Q23.1) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(12Q23.1) MUTATED                          14
  DEL PEAK 27(12Q23.1) WILD-TYPE                        76
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 27(12Q23.1) MUTATED                                           0
  DEL PEAK 27(12Q23.1) WILD-TYPE                                         9
                                vv
clus                             WHITE
  DEL PEAK 27(12Q23.1) MUTATED      25
  DEL PEAK 27(12Q23.1) WILD-TYPE   332
D78V6, multiclass
                                           clus
vv                                          DEL PEAK 27(12Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               25
                                           clus
vv                                          DEL PEAK 27(12Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              9
  WHITE                                                                332
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12Q23.1) MUTATED     1  28
  DEL PEAK 27(12Q23.1) WILD-TYPE  12 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12Q23.1) MUTATED      1   28
  DEL PEAK 27(12Q23.1) WILD-TYPE   12  322
                        clus
vv                       DEL PEAK 27(12Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           28
                        clus
vv                       DEL PEAK 27(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            322
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 28(12Q24.33) MUTATION ANALYSIS
D79V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(12Q24.33) MUTATED    46  10
  DEL PEAK 28(12Q24.33) WILD-TYPE 397  50
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             56                             447 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             10                              50 
$`DEL PEAK 28(12Q24.33) MUTATED`
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23N 
       11.44        36.33        91.04        28.64        14.96         1.08 
TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AP-A052 
        0.85         2.24         0.92         1.35         0.76        21.99 
TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A1C7 
       45.53        97.71        33.40        18.25         0.56        16.96 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3G3 TCGA-B5-A0JN 
       12.43        76.83         4.77        71.24         0.03        80.38 
TCGA-B5-A0K8 TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A139 
       17.85         5.03        34.95        12.56        15.45        10.16 
TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1O0 
       24.13        22.55        39.48        18.67        28.08         2.07 
TCGA-D1-A3DH TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 
        4.11        12.39        31.10        91.96        48.36        10.92 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A214 TCGA-EY-A2OQ 
       34.39        27.16        16.34         4.54        14.40        29.10 
TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2EU TCGA-FI-A3PV TCGA-K6-A3WQ 
        6.44         3.72         5.88        96.69        41.06        13.15 
TCGA-PG-A7D5 TCGA-PG-A915 
       23.97         7.00 

$`DEL PEAK 28(12Q24.33) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       65.75        60.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       28.27        20.81        23.21        68.65        19.96        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         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60         8.02        46.32         5.33         5.16         7.33 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.18         1.97         0.39        19.79         2.40         3.02 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        0.49         1.12         0.76         1.68         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         1.28        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        0.99         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       82.52        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       33.73        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CE TCGA-AX-A1CI 
       19.20        13.55        15.25        20.28        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39        11.08        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       33.53        61.18        68.71        33.40        40.50        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        27.32         2.96        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.10         0.33         0.13         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.13         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E 
       17.88        13.74        17.10        11.01         4.11         8.71 
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        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       43.96        40.50        36.82        32.09        33.50        27.35 
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 
      191.84       102.31        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.87        15.29        12.79       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.22        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        23.47        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 
       67.20        88.34        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        62.79        63.58        49.55        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        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-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         1.41         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         6.77         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        35.38         9.37        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        24.33        16.01         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       18.81        37.71        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        24.79        32.38        19.40        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       12.89        26.96        22.26         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR 
       13.97         6.90        19.27        18.84        17.88        17.62 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       15.09        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        12.59         3.62        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        27.35        13.84        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         5.29        40.01        34.98        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        7.99        13.84         8.98        59.01         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.96        25.02        26.01        45.01         1.74         2.43 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       10.82         9.11        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                          97.71                          191.84 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                          16.65                           23.34 
[1] "0.0 - 97.7 (16.6)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "2"  
D79V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 28(12Q24.33) MUTATED                                        16
  DEL PEAK 28(12Q24.33) WILD-TYPE                                     364
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 28(12Q24.33) MUTATED                               2
  DEL PEAK 28(12Q24.33) WILD-TYPE                            19
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 28(12Q24.33) MUTATED                                  38
  DEL PEAK 28(12Q24.33) WILD-TYPE                                66
D79V3, multiclass
                                         clus
vv                                        DEL PEAK 28(12Q24.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            16
  MIXED SEROUS AND ENDOMETRIOID                                       2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  38
                                         clus
vv                                        DEL PEAK 28(12Q24.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             364
  MIXED SEROUS AND ENDOMETRIOID                                        19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q24.33) MUTATED     9  47
  DEL PEAK 28(12Q24.33) WILD-TYPE 129 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED      9   47
  DEL PEAK 28(12Q24.33) WILD-TYPE  129  320
     clus
vv    DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  NO                              9                             129
  YES                            47                             320
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(12Q24.33) MUTATED    35   2   5   6
  DEL PEAK 28(12Q24.33) WILD-TYPE 316  20  12  24
D79V5, multiclass
    clus
vv   DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  R0                            35                             316
  R1                             2                              20
  R2                             5                              12
  RX                             6                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(12Q24.33) MUTATED                                  1     1
  DEL PEAK 28(12Q24.33) WILD-TYPE                                3    18
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(12Q24.33) MUTATED                          13
  DEL PEAK 28(12Q24.33) WILD-TYPE                        77
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 28(12Q24.33) MUTATED                                           0
  DEL PEAK 28(12Q24.33) WILD-TYPE                                         9
                                 vv
clus                              WHITE
  DEL PEAK 28(12Q24.33) MUTATED      36
  DEL PEAK 28(12Q24.33) WILD-TYPE   321
D79V6, multiclass
                                           clus
vv                                          DEL PEAK 28(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                            13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                36
                                           clus
vv                                          DEL PEAK 28(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  18
  BLACK OR AFRICAN AMERICAN                                              77
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               9
  WHITE                                                                 321
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q24.33) MUTATED     1  39
  DEL PEAK 28(12Q24.33) WILD-TYPE  12 311
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED      1   39
  DEL PEAK 28(12Q24.33) WILD-TYPE   12  311
                        clus
vv                       DEL PEAK 28(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            39
                        clus
vv                       DEL PEAK 28(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             311
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 29(13Q11) MUTATION ANALYSIS
D80V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 29(13Q11) MUTATED    69  17
  DEL PEAK 29(13Q11) WILD-TYPE 374  43
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          86                          417 
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          17                           43 
$`DEL PEAK 29(13Q11) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OH 
      149.56        65.75        60.53        17.59        42.35        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QM 
       91.04        28.64         7.33        14.96         0.39         0.85 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AJ-A3QS 
        2.24         1.64        22.26         1.28         0.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
        1.71         0.99        45.53        20.91        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1C9 
       97.71        33.40        33.73        53.92        16.96        15.25 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HF TCGA-AX-A2HK 
       20.28        76.83        36.39        30.12        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0KB 
       38.70        20.52         0.03         0.13         0.13         4.11 
TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A5OE 
       36.82        50.89        11.87        12.79       116.25        34.95 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD 
        7.92        12.56        15.45         6.81        10.16        16.64 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A1NU 
       61.87        67.20        37.32        31.07         6.77        13.22 
TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        4.27        35.38         9.37        91.96        10.92        18.81 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW 
       32.38        27.16        18.84        17.62        15.81         8.55 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       13.45        45.76        29.10        13.84         6.44        17.92 
TCGA-FI-A2D4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-PG-A5BC 
        7.99        25.02        41.06        45.01         2.43        10.82 
TCGA-PG-A7D5 TCGA-PG-A914 
       23.97        12.92 

$`DEL PEAK 29(13Q11) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ 
       68.65        19.96        19.59        24.62        29.06        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
        7.92        11.44         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16         1.18         1.08         1.97        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        3.02         0.49         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
        1.94        15.95         1.87         2.33         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0LD 
       39.42        57.80        36.89         7.86        12.20       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       27.12        82.52        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        18.25         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       34.98        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       13.28        19.20        13.55        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       54.12        67.50        25.12        11.08         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       33.53        61.18        68.71        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       17.75        27.32        31.13         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13         0.20         0.23         1.18         8.35        14.47 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        8.71       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 
       45.90        43.96        40.50        32.09        33.50        27.35 
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 
      191.84       102.31        14.40        14.70        11.70        15.29 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11         5.03        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-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
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-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        10.22        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        23.47        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 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         1.41         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-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.11        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        48.36 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        24.33        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        37.71        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        24.79        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        26.96        22.26        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       23.90        22.78        13.97         6.90        19.27        17.88 
TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       15.09        16.11        12.43         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 
        3.62        14.40        18.87        22.82        31.04        27.35 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
        2.14         6.97         3.72         5.29         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       34.98        33.99        36.00        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR 
       59.01         9.07        28.93        28.96        26.01         1.74 
TCGA-K6-A3WQ TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       13.15         9.11         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                        0.03                         0.10 
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                      149.56                       191.84 
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                      18.365                       23.380 
[1] "0.0 - 149.6 (18.4)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2"  
D80V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 29(13Q11) MUTATED                                        36
  DEL PEAK 29(13Q11) WILD-TYPE                                     344
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 29(13Q11) MUTATED                               5
  DEL PEAK 29(13Q11) WILD-TYPE                            16
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 29(13Q11) MUTATED                                  45
  DEL PEAK 29(13Q11) WILD-TYPE                                59
D80V3, multiclass
                                         clus
vv                                        DEL PEAK 29(13Q11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         36
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               45
                                         clus
vv                                        DEL PEAK 29(13Q11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          344
  MIXED SEROUS AND ENDOMETRIOID                                     16
  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"
D80V4, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q11) MUTATED    17  69
  DEL PEAK 29(13Q11) WILD-TYPE 121 298
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q11) MUTATED     17   69
  DEL PEAK 29(13Q11) WILD-TYPE  121  298
     clus
vv    DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE
  NO                          17                          121
  YES                         69                          298
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 29(13Q11) MUTATED    56   5   6   6
  DEL PEAK 29(13Q11) WILD-TYPE 295  17  11  24
D80V5, multiclass
    clus
vv   DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE
  R0                         56                          295
  R1                          5                           17
  R2                          6                           11
  RX                          6                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(13Q11) MUTATED                                  0     3
  DEL PEAK 29(13Q11) WILD-TYPE                                4    16
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(13Q11) MUTATED                          23
  DEL PEAK 29(13Q11) WILD-TYPE                        67
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 29(13Q11) MUTATED                                           2    55
  DEL PEAK 29(13Q11) WILD-TYPE                                         7   302
D80V6, multiclass
                                           clus
vv                                          DEL PEAK 29(13Q11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              3
  BLACK OR AFRICAN AMERICAN                                         23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             55
                                           clus
vv                                          DEL PEAK 29(13Q11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                           67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  WHITE                                                              302
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q11) MUTATED     4  60
  DEL PEAK 29(13Q11) WILD-TYPE   9 290
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q11) MUTATED      4   60
  DEL PEAK 29(13Q11) WILD-TYPE    9  290
                        clus
vv                       DEL PEAK 29(13Q11) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       DEL PEAK 29(13Q11) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          290
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 30(13Q14.2) MUTATION ANALYSIS
D81V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(13Q14.2) MUTATED    76  16
  DEL PEAK 30(13Q14.2) WILD-TYPE 367  44
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            92                            411 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            16                             44 
$`DEL PEAK 30(13Q14.2) MUTATED`
TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A0VP 
        1.08       149.56        65.75        60.53        17.59        42.35 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A2QM 
       36.33        91.04         7.33        14.96         0.39         0.85 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AJ-A3QS 
        2.24         1.64        22.26         1.28         0.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0LI TCGA-AP-A0LO 
        1.71         0.99        45.53        20.91        97.71        33.40 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C9 TCGA-AX-A1CF TCGA-AX-A1CK 
       33.73         0.56        53.92        15.25        76.83        67.50 
TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       36.39        30.12         2.96         0.33         0.13        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11P 
        0.03         0.13         0.13        23.01         4.11        36.82 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE 
       50.89        11.87        12.79       116.25        33.11        34.95 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0CC 
        7.92        12.56        15.45        23.70         6.81        10.22 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16N 
       10.16        16.64        61.87        67.20        37.32        31.07 
TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A3DG TCGA-DI-A1NN 
        1.41         6.77        28.08        13.22         4.27        35.38 
TCGA-DI-A1NO TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GC 
        9.37        24.33        18.81        34.39        27.16         4.54 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON 
       18.84        17.62        15.81         8.55        12.59        13.45 
TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-FI-A2EX TCGA-FI-A2EY 
       45.76        29.10        13.84        17.92         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        26.01        41.06        45.01        13.15         2.43 
TCGA-PG-A5BC TCGA-PG-A7D5 
       10.82        23.97 

$`DEL PEAK 30(13Q14.2) WILD-TYPE`
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         3.22 
TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP 
      105.37        87.32        74.10        57.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       38.37        36.82        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.96        19.59        24.62        29.06        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       11.44         9.60         8.02        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16         1.18         1.08         1.97        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        3.02         0.49         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
        1.94        15.95         1.87         2.33         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
       83.67        21.99         5.95        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 
       39.42        57.80        36.89         7.86        12.20        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
      125.42       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ 
       31.73        83.97        27.12        82.52        61.64        80.78 
TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24        18.25        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       65.88        13.28        19.20        16.96        13.55        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CR 
       12.43        20.05        72.56        54.12        25.12        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 
       38.70         0.23         0.10         0.20         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        8.35        14.47        80.38        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84       102.31        14.40        14.70        11.70 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC 
       15.29        96.30        78.81        62.14         5.03        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-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
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-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       35.67        20.12        11.31        35.90        34.98         6.21 
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        23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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-A16S 
       11.51        29.92        33.63        10.65         0.69        18.67 
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-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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ 
       41.42         8.48        44.88         0.26         4.11        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 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.01         7.36        16.80        10.92        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       35.05        33.01        27.12        57.60        24.79        32.38 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.40        19.36        35.15        12.89        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       23.34        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX 
       19.27        17.88        15.09        16.11        12.43         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
       19.33         3.62        14.40        18.87        22.82        31.04 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35         6.44         2.14         6.97         3.72         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        34.98        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-H5-A2HR 
       13.84         8.98        96.69        59.01        28.96         1.74 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        9.11        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                        149.56                         191.84 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                        17.605                         23.470 
[1] "0.0 - 149.6 (17.6)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.9"
D81V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                        48
  DEL PEAK 30(13Q14.2) WILD-TYPE                                     332
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 30(13Q14.2) MUTATED                               6
  DEL PEAK 30(13Q14.2) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                  39
  DEL PEAK 30(13Q14.2) WILD-TYPE                                65
D81V3, multiclass
                                         clus
vv                                        DEL PEAK 30(13Q14.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           48
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 39
                                         clus
vv                                        DEL PEAK 30(13Q14.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            332
  MIXED SEROUS AND ENDOMETRIOID                                       15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V4, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED    16  77
  DEL PEAK 30(13Q14.2) WILD-TYPE 122 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     16   77
  DEL PEAK 30(13Q14.2) WILD-TYPE  122  290
     clus
vv    DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  NO                            16                            122
  YES                           77                            290
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(13Q14.2) MUTATED    60   2   5   5
  DEL PEAK 30(13Q14.2) WILD-TYPE 291  20  12  25
D81V5, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  R0                           60                            291
  R1                            2                             20
  R2                            5                             12
  RX                            5                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(13Q14.2) MUTATED                                  0     2
  DEL PEAK 30(13Q14.2) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(13Q14.2) MUTATED                          25
  DEL PEAK 30(13Q14.2) WILD-TYPE                        65
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 30(13Q14.2) MUTATED                                           2
  DEL PEAK 30(13Q14.2) WILD-TYPE                                         7
                                vv
clus                             WHITE
  DEL PEAK 30(13Q14.2) MUTATED      61
  DEL PEAK 30(13Q14.2) WILD-TYPE   296
D81V6, multiclass
                                           clus
vv                                          DEL PEAK 30(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               61
                                           clus
vv                                          DEL PEAK 30(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                296
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED     5  69
  DEL PEAK 30(13Q14.2) WILD-TYPE   8 281
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED      5   69
  DEL PEAK 30(13Q14.2) WILD-TYPE    8  281
                        clus
vv                       DEL PEAK 30(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 30(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            281
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 31(14Q13.1) MUTATION ANALYSIS
D82V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(14Q13.1) MUTATED    54  12
  DEL PEAK 31(14Q13.1) WILD-TYPE 389  48
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            66                            437 
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            12                             48 
$`DEL PEAK 31(14Q13.1) MUTATED`
TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A2QM 
       60.53        19.96        17.59        28.64         1.18         0.85 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EL TCGA-AJ-A3NH TCGA-AJ-A6NU 
        0.49         2.24         1.64        22.49         0.76         0.99 
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        30.90        37.78 
TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3G1 
       20.28        11.08         4.77         2.96         0.33        20.52 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11P 
        0.23         0.13        80.38        17.85         4.11        36.82 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BK-A0CC 
       11.87        12.79         5.03        34.13        15.45        10.22 
TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW 
       10.16        16.64        11.51         6.77        13.22         0.72 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3KU 
       35.38        12.39        24.33        32.38        34.39        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A214 
       16.34        23.90        19.27        17.62        15.09        14.40 
TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU 
       45.76        29.10         6.44         3.72        34.98        96.69 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A7D5 TCGA-PG-A915 
       25.02        26.01        45.01         1.74        23.97         7.00 

$`DEL PEAK 31(14Q13.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       20.81        23.21        68.65        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         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        8.02        91.04        46.32         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       14.96         1.08         1.97         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EM 
        3.02         1.12         0.76         1.68        14.66        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
        1.28         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
        2.70         0.13        83.67        21.99         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG 
       12.20        20.91       117.99       110.37         3.39        63.16 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
       36.36        97.71        31.73        83.97        27.12        82.52 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
        6.71        10.42        27.85        16.24        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 
       28.54        43.82        40.11        65.88        13.28        19.20 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       16.96        13.55        15.25        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 
       72.56        54.12        67.50        25.12        36.39        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.23         0.10         0.13         0.20         0.03         0.13 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       11.01         8.71       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        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.70        15.29       116.25        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       33.11        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
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        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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        62.79        63.58        49.55        63.16        66.48 
TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       16.83        19.79        29.95         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
       28.67        23.93        22.55         1.74         4.44        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         1.41         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-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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       44.88         0.26         4.27         4.11        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        36.62        24.30         9.37        31.10        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       35.05        33.01        27.12        57.60        24.79        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 
       19.36        35.15        12.89        27.16        26.96         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.34        22.78        13.97         6.90        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81         8.55         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       12.59         3.62        18.87        22.82        13.45        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       27.35        13.84        17.92         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV 
        8.98        59.01         9.07        28.93        28.96        41.06 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
       13.15         2.43        10.82         9.11        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                        17.115                         23.470 
[1] "0.1 - 125.4 (17.1)" "0.0 - 191.8 (23.5)"
[1] "hr=" "2.2"
D82V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 31(14Q13.1) MUTATED                                        24
  DEL PEAK 31(14Q13.1) WILD-TYPE                                     356
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 31(14Q13.1) MUTATED                               5
  DEL PEAK 31(14Q13.1) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 31(14Q13.1) MUTATED                                  38
  DEL PEAK 31(14Q13.1) WILD-TYPE                                66
D82V3, multiclass
                                         clus
vv                                        DEL PEAK 31(14Q13.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           24
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        DEL PEAK 31(14Q13.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            356
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V4, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q13.1) MUTATED    15  52
  DEL PEAK 31(14Q13.1) WILD-TYPE 123 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q13.1) MUTATED     15   52
  DEL PEAK 31(14Q13.1) WILD-TYPE  123  315
     clus
vv    DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE
  NO                            15                            123
  YES                           52                            315
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(14Q13.1) MUTATED    43   3   2   3
  DEL PEAK 31(14Q13.1) WILD-TYPE 308  19  15  27
D82V5, multiclass
    clus
vv   DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE
  R0                           43                            308
  R1                            3                             19
  R2                            2                             15
  RX                            3                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(14Q13.1) MUTATED                                  1     1
  DEL PEAK 31(14Q13.1) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(14Q13.1) MUTATED                          22
  DEL PEAK 31(14Q13.1) WILD-TYPE                        68
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 31(14Q13.1) MUTATED                                           1
  DEL PEAK 31(14Q13.1) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK 31(14Q13.1) MUTATED      37
  DEL PEAK 31(14Q13.1) WILD-TYPE   320
D82V6, multiclass
                                           clus
vv                                          DEL PEAK 31(14Q13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               37
                                           clus
vv                                          DEL PEAK 31(14Q13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                320
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q13.1) MUTATED     3  43
  DEL PEAK 31(14Q13.1) WILD-TYPE  10 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q13.1) MUTATED      3   43
  DEL PEAK 31(14Q13.1) WILD-TYPE   10  307
                        clus
vv                       DEL PEAK 31(14Q13.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       DEL PEAK 31(14Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            307
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 32(15Q15.1) MUTATION ANALYSIS
D83V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q15.1) MUTATED   103  24
  DEL PEAK 32(15Q15.1) WILD-TYPE 340  36
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           127                            376 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                            24                             36 
$`DEL PEAK 32(15Q15.1) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       65.75        60.53        19.96        17.59        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK 
       91.04        46.32        28.64         7.33        14.96         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA 
        0.85         0.49         2.24         1.64        22.26         0.92 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 
        1.35         0.76        16.87         0.99        21.99         5.95 
TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       45.53        97.71        41.95        18.25        33.73         0.56 
TCGA-AX-A060 TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       35.34        53.92        37.78        15.25        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
       76.83        11.08        30.12        61.18        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
       38.70         0.23         0.20        20.52         0.03         0.13 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        0.13        80.38        23.01        17.85         4.11        75.72 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
       36.82       102.31        50.89        11.87        12.79       116.25 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A139 
        5.03        34.95        36.49        12.56        15.45        10.16 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP 
       24.13        16.64        61.87        67.20        49.55        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S 
        8.55        22.55        37.32        11.51        31.07        18.67 
TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DG 
        1.41         6.77        13.22         0.72         2.07         4.27 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        4.11        35.38         9.37        31.10        91.96        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       24.33        10.92        37.71        32.38        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO 
       27.16        26.96        22.26        16.34         4.54        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       18.84        15.09         8.55        12.59         3.62        14.40 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 
       13.45        45.76        29.10        27.35         6.44        17.92 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       36.00        96.69        59.01        28.93        25.02        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 
       41.06        45.01        13.15        10.82        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`DEL PEAK 32(15Q15.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 
       15.95         7.92         9.60         8.02         5.33         5.16 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.18         1.08         1.97        19.79         2.40         3.02 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
        1.12         0.76         1.68        14.66        22.49         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62         1.94        15.95         1.87 
TCGA-AJ-A3TW TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
        1.71         2.33         2.70         0.13        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N 
       86.07         8.22        39.42        57.80        36.89         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       12.20        20.91        48.79       125.42       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        19.82        29.69        68.35        72.03        46.45 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE 
       65.88        13.28        19.20        16.96        13.55        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        36.39         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        33.53        68.71        33.40        40.50        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       17.75        27.32        31.13         0.10         0.33         0.13 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.23         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       11.01         8.71       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 
       45.90        43.96        40.50        32.09        33.50        27.35 
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-A3FA 
      191.84        14.40        14.70        11.70        15.29        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       78.81        62.14        33.11        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98         7.92 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.22        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        23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZR 
       63.58        63.16        66.48        16.83        19.79         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        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-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26        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        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
        6.67        16.01         7.36        16.80        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       35.05        33.01        27.12        57.60        24.79        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       35.15        12.89         6.21        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL 
       27.16        23.34        23.34        23.90        22.78        13.97 
TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
        6.90        17.88        17.62        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3QX 
        6.48        19.33        18.87        22.82        31.04        13.84 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
        2.14         6.97         3.72         5.29         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX 
       34.98        33.99         7.99        13.84         8.98         9.07 
TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       28.96         1.74         2.43         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                        116.25                         191.84 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                        19.360                         23.585 
[1] "0.0 - 116.2 (19.4)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.3"
D83V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                        49
  DEL PEAK 32(15Q15.1) WILD-TYPE                                     331
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 32(15Q15.1) MUTATED                               9
  DEL PEAK 32(15Q15.1) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                  70
  DEL PEAK 32(15Q15.1) WILD-TYPE                                34
D83V3, multiclass
                                         clus
vv                                        DEL PEAK 32(15Q15.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           49
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 70
                                         clus
vv                                        DEL PEAK 32(15Q15.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            331
  MIXED SEROUS AND ENDOMETRIOID                                       12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V4, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.1) MUTATED    24 104
  DEL PEAK 32(15Q15.1) WILD-TYPE 114 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED     24  104
  DEL PEAK 32(15Q15.1) WILD-TYPE  114  263
     clus
vv    DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  NO                            24                            114
  YES                          104                            263
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q15.1) MUTATED    79   7   8  11
  DEL PEAK 32(15Q15.1) WILD-TYPE 272  15   9  19
D83V5, multiclass
    clus
vv   DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  R0                           79                            272
  R1                            7                             15
  R2                            8                              9
  RX                           11                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(15Q15.1) MUTATED                                  1     2
  DEL PEAK 32(15Q15.1) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(15Q15.1) MUTATED                          32
  DEL PEAK 32(15Q15.1) WILD-TYPE                        58
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 32(15Q15.1) MUTATED                                           3
  DEL PEAK 32(15Q15.1) WILD-TYPE                                         6
                                vv
clus                             WHITE
  DEL PEAK 32(15Q15.1) MUTATED      80
  DEL PEAK 32(15Q15.1) WILD-TYPE   277
D83V6, multiclass
                                           clus
vv                                          DEL PEAK 32(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               80
                                           clus
vv                                          DEL PEAK 32(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                277
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.1) MUTATED     3  91
  DEL PEAK 32(15Q15.1) WILD-TYPE  10 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED      3   91
  DEL PEAK 32(15Q15.1) WILD-TYPE   10  259
                        clus
vv                       DEL PEAK 32(15Q15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           91
                        clus
vv                       DEL PEAK 32(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            259
[1] 2 2
[1] FALSE

Clustering(84) Variable = DEL PEAK 33(15Q23) MUTATION ANALYSIS
D84V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 33(15Q23) MUTATED    89  17
  DEL PEAK 33(15Q23) WILD-TYPE 354  43
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                         106                          397 
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                          17                           43 
$`DEL PEAK 33(15Q23) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 
       65.75        60.53        19.96        17.59        11.44        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK 
       46.32        28.64         7.33        14.96         1.08         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        0.85         0.49         1.12         2.24         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
        0.92         1.35         0.76        16.87         1.71         0.99 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 TCGA-AP-A5FX 
       21.99        45.53        48.79       125.42        18.25        33.73 
TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
        0.56        53.92        37.78        15.25        20.28        12.43 
TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO 
       11.08        30.12        61.18        19.36         2.96        38.70 
TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         0.20         0.03         0.23         0.13        80.38 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY 
       17.85         4.11        75.72        36.82       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3S1 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A18C 
       12.79       116.25         5.03        36.49        21.17        15.45 
TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZQ 
        6.81        24.13        16.64        61.87        67.20         8.55 
TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A1NU 
       22.55        11.51        31.07        18.67         1.41        13.22 
TCGA-D1-A3DH TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 
        4.11         9.37        48.36        24.33        10.92        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       32.38        19.40        27.16        26.96        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A214 
        4.54        19.27        18.84        15.09         3.62        14.40 
TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2D2 
       45.76        27.35         6.44        17.92         3.72        36.00 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-K6-A3WQ 
       96.69        59.01        28.93        25.02         1.74        13.15 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       10.82        23.97        12.92         7.00 

$`DEL PEAK 33(15Q23) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK TCGA-A5-A2K5 
       15.95         7.92        36.33         9.60         8.02         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        5.16         1.18         1.97        19.79         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC 
        0.76         1.68        14.66        22.49         1.28        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW 
       20.65        15.62         1.94        15.95         1.87         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       97.71        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR 
       60.36        55.89        31.30        35.54        41.95        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S 
        6.71        30.90        10.42        27.85        16.24        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CE 
       65.88        13.28        19.20        16.96        13.55        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       76.83        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
        4.77        71.24        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW 
       26.33        17.75        27.32        31.13         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.13        20.52         0.13         1.18         8.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       32.55        28.64        28.34        30.51        25.91        23.01 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F 
       17.88        13.74        17.10        11.01         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        11.70        15.29        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       43.04        39.32        30.81        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        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         6.21        10.22        10.16 
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-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ 
       23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       49.55        63.16        66.48        16.83        19.79        29.95 
TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 
        0.56         4.87        28.67        23.93         1.74         4.44 
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-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-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02         6.77         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-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        1.41         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        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        91.96 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        18.81        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        24.79        34.39        19.36        35.15        12.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ 
       23.34        23.90        22.78        13.97         6.90        17.88 
TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        12.43        15.81         8.55         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
       19.33        12.59        18.87        22.82        13.45        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       29.10        13.84         2.14         6.97         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 
        9.07        28.96        26.01        41.06        45.01         2.43 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        9.11        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                        0.03                         0.10 
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                      125.42                       191.84 
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                       17.72                        24.36 
[1] "0.0 - 125.4 (17.7)" "0.1 - 191.8 (24.4)"
[1] "hr=" "1.8"
D84V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 33(15Q23) MUTATED                                        37
  DEL PEAK 33(15Q23) WILD-TYPE                                     343
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 33(15Q23) MUTATED                               7
  DEL PEAK 33(15Q23) WILD-TYPE                            14
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 33(15Q23) MUTATED                                  63
  DEL PEAK 33(15Q23) WILD-TYPE                                41
D84V3, multiclass
                                         clus
vv                                        DEL PEAK 33(15Q23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         37
  MIXED SEROUS AND ENDOMETRIOID                                    7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               63
                                         clus
vv                                        DEL PEAK 33(15Q23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          343
  MIXED SEROUS AND ENDOMETRIOID                                     14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V4, binary
                              cls
clus                             0   1
  DEL PEAK 33(15Q23) MUTATED    22  85
  DEL PEAK 33(15Q23) WILD-TYPE 116 282
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(15Q23) MUTATED     22   85
  DEL PEAK 33(15Q23) WILD-TYPE  116  282
     clus
vv    DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE
  NO                          22                          116
  YES                         85                          282
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 33(15Q23) MUTATED    71   4   6   8
  DEL PEAK 33(15Q23) WILD-TYPE 280  18  11  22
D84V5, multiclass
    clus
vv   DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE
  R0                         71                          280
  R1                          4                           18
  R2                          6                           11
  RX                          8                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(15Q23) MUTATED                                  0     2
  DEL PEAK 33(15Q23) WILD-TYPE                                4    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(15Q23) MUTATED                          29
  DEL PEAK 33(15Q23) WILD-TYPE                        61
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 33(15Q23) MUTATED                                           1    66
  DEL PEAK 33(15Q23) WILD-TYPE                                         8   291
D84V6, multiclass
                                           clus
vv                                          DEL PEAK 33(15Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             66
                                           clus
vv                                          DEL PEAK 33(15Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            8
  WHITE                                                              291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D84V7, binary
                              cls
clus                             0   1
  DEL PEAK 33(15Q23) MUTATED     1  76
  DEL PEAK 33(15Q23) WILD-TYPE  12 274
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(15Q23) MUTATED      1   76
  DEL PEAK 33(15Q23) WILD-TYPE   12  274
                        clus
vv                       DEL PEAK 33(15Q23) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         76
                        clus
vv                       DEL PEAK 33(15Q23) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          274
[1] 2 2
[1] FALSE

Clustering(85) Variable = DEL PEAK 34(16P13.3) MUTATION ANALYSIS
D85V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16P13.3) MUTATED    67  15
  DEL PEAK 34(16P13.3) WILD-TYPE 376  45
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            82                            421 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            15                             45 
$`DEL PEAK 34(16P13.3) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO 
       37.02        60.53        11.44        36.33        28.64         7.33 
TCGA-AJ-A23M TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW 
        1.18         0.85         1.12         0.92         0.76         1.71 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ 
       21.99        45.53        48.79       125.42        97.71        41.95 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       18.25         0.56        53.92        13.55        15.25        12.43 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2IO 
       76.83        11.08         4.77        30.12        71.24        38.70 
TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.03         0.13        43.13        23.01        17.85         4.11 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A3S1 
       75.72        36.82       102.31        11.87        33.11         5.03 
TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD 
       34.95        15.45         6.81        10.22        10.16        16.64 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU 
       49.55        22.55        11.51        31.07        18.67        13.22 
TCGA-D1-A1NW TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
        0.72         4.27         4.11        35.38         9.37        91.96 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ 
       24.33        10.92        18.81        37.71        32.38        27.16 
TCGA-EO-A3B1 TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A3L3 
       26.96        17.62        12.59         3.62        29.10        27.35 
TCGA-EY-A3QX TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       13.84        96.69        28.93        41.06        45.01         1.74 
TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
        2.43        10.82        23.97         7.00 

$`DEL PEAK 34(16P13.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 
       23.21        68.65        19.96        17.59        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23N 
       91.04        46.32         5.33         5.16        14.96         1.08 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        1.97         0.39        19.79         2.40         3.02         0.49 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         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         1.28        36.99        20.65         1.35        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU 
        1.94        15.95         1.87        16.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        57.80        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       117.99       110.37         3.39        63.16        36.36 
TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       31.73        83.97        27.12        82.52        33.40        61.64 
TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK 
       80.78        63.06        49.22        25.08        71.67        60.36 
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        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        16.24        33.73        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       60.66        35.01        28.54        37.78        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CE 
       65.88        13.28        19.20        16.96        20.28        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H7 
       72.56        54.12        67.50        25.12        36.39        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        27.32         2.96        31.13         0.23         0.10 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.33         0.13         0.20        20.52         0.13         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 
       50.89        14.40        14.70        11.70        15.29        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD 
      116.25        96.30        78.81        62.14        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        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-A56F 
       34.98         6.21        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        23.47        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        67.20        88.34        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        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       66.48        16.83        19.79        29.95         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        0.26        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        31.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        6.67        16.01         7.36        16.80        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       33.01        27.12        57.60        24.79        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        35.15        12.89        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       18.84        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       13.45        45.76        31.04         6.44        17.92         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
        6.97         3.72         5.29         5.88        40.01        34.98 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       33.99        36.00         7.99        13.84         8.98        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-PG-A6IB 
        9.07        28.96        25.02        26.01        13.15         9.11 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       12.92        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                         18.46                          23.34 
[1] "0.0 - 125.4 (18.5)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.9"
D85V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 34(16P13.3) MUTATED                                        24
  DEL PEAK 34(16P13.3) WILD-TYPE                                     356
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 34(16P13.3) MUTATED                               5
  DEL PEAK 34(16P13.3) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 34(16P13.3) MUTATED                                  54
  DEL PEAK 34(16P13.3) WILD-TYPE                                50
D85V3, multiclass
                                         clus
vv                                        DEL PEAK 34(16P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           24
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 54
                                         clus
vv                                        DEL PEAK 34(16P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            356
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V4, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    17  66
  DEL PEAK 34(16P13.3) WILD-TYPE 121 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     17   66
  DEL PEAK 34(16P13.3) WILD-TYPE  121  301
     clus
vv    DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  NO                            17                            121
  YES                           66                            301
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16P13.3) MUTATED    50   6   5   6
  DEL PEAK 34(16P13.3) WILD-TYPE 301  16  12  24
D85V5, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  R0                           50                            301
  R1                            6                             16
  R2                            5                             12
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(16P13.3) MUTATED                                  0     2
  DEL PEAK 34(16P13.3) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(16P13.3) MUTATED                          25
  DEL PEAK 34(16P13.3) WILD-TYPE                        65
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 34(16P13.3) MUTATED                                           1
  DEL PEAK 34(16P13.3) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK 34(16P13.3) MUTATED      49
  DEL PEAK 34(16P13.3) WILD-TYPE   308
D85V6, multiclass
                                           clus
vv                                          DEL PEAK 34(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               49
                                           clus
vv                                          DEL PEAK 34(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                308
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED     2  54
  DEL PEAK 34(16P13.3) WILD-TYPE  11 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED      2   54
  DEL PEAK 34(16P13.3) WILD-TYPE   11  296
                        clus
vv                       DEL PEAK 34(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 34(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(86) Variable = DEL PEAK 35(16Q21) MUTATION ANALYSIS
D86V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 35(16Q21) MUTATED   118  22
  DEL PEAK 35(16Q21) WILD-TYPE 325  38
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                         140                          363 
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                          22                           38 
$`DEL PEAK 35(16Q21) MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       87.32        65.75        60.53        17.59        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       91.04        28.64         7.33        14.96         1.18         1.08 
TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH 
        0.39         0.85         0.49        22.26         1.35         0.76 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H 
        1.71         0.99        21.99         5.95        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO 
       36.89        48.79         3.39        97.71        41.95         0.56 
TCGA-AX-A05U TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C9 
       29.69        53.92        28.54        37.78        16.96        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       20.28        12.43        72.56        25.12        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HK 
       30.12        71.24        61.18        40.50        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       38.70         0.33         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K6 TCGA-B5-A0K8 
        0.13         0.23         0.13        43.13        13.74        17.85 
TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY 
        4.11       113.36        75.72        36.82       102.31        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 
       12.79        33.11         5.03        34.95         7.92        36.49 
TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C 
       20.28        24.39        16.34        12.56        13.78        15.45 
TCGA-BG-A2AE TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V 
       23.70        16.64        61.87        49.55        22.55        39.48 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K 
       27.42        11.51        29.92        31.07         6.77        28.08 
TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG 
       11.15        13.22         0.72        18.25         2.07         4.27 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        4.11        35.38         9.37        31.10        91.96        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       24.33        10.92        18.81        37.71        32.38        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         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 
       23.90         6.90        17.62        15.09        15.81        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
        3.62        14.40        29.10        27.35        13.84         6.44 
TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       17.92         3.72        34.98        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 
       28.93        25.02        41.06        45.01         1.74         2.43 
TCGA-PG-A7D5 TCGA-PG-A915 
       23.97         7.00 

$`DEL PEAK 35(16Q21) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
       32.78         3.22       105.37        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       46.55        38.37        36.82        28.27        20.81        23.21 
TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       68.65        19.96        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95         7.92         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        5.16         1.97        19.79         2.40         3.02         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
        1.28         0.92        36.99        20.65        15.62         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
       15.95         1.87        16.87         2.33         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N 
       83.67        23.31        86.07         8.22        39.42         7.86 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91       125.42       117.99       110.37        63.16 
TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO 
       36.36        31.73        83.97        27.12        82.52        33.40 
TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH 
       61.64        80.78        63.06        49.22        25.08        71.67 
TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        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 
       30.90        10.42        27.85        16.24        18.25        33.73 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       30.02        60.66        35.01        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ 
       13.28        19.20        13.55        20.05        76.83        54.12 
TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG 
       67.50         4.77        33.53        68.71        33.40        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 
       17.75        27.32        31.13         0.23         0.10         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        8.35        14.47        80.38        56.91        46.75        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       25.91        23.01        17.88        17.10        11.01         8.71 
TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O 
      185.79        88.34        54.44        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14        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        34.98        38.37        28.27        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        39.32 
TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ 
       30.81        21.17        15.42        26.66        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        35.67        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        35.90        34.98         6.21        10.22        10.16 
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        23.47        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        67.20        88.34 
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-A0ZO 
       62.79        63.58        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-A16O TCGA-D1-A16Q 
       37.32        36.36        37.51        36.79        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         1.41         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-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY 
        1.78        24.30         2.33        22.92         1.41        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26        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        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        6.67        16.01         7.36        16.80        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       33.01        27.12        57.60        24.79        19.36        35.15 
TCGA-EO-A3AY TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       12.89         6.21        14.99         8.15        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        22.78        13.97        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       17.88        16.11        12.43         8.55         6.48        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 
       18.87        22.82        13.45        45.76        31.04         2.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         5.29         5.88        40.01        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-K6-A3WQ 
        7.99        13.84         8.98        28.96        26.01        13.15 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       10.82         9.11        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                        0.03                         0.10 
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                      113.36                       191.84 
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                       19.38                        23.47 
[1] "0.0 - 113.4 (19.4)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.8"
D86V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 35(16Q21) MUTATED                                        59
  DEL PEAK 35(16Q21) WILD-TYPE                                     321
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 35(16Q21) MUTATED                               8
  DEL PEAK 35(16Q21) WILD-TYPE                            13
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 35(16Q21) MUTATED                                  74
  DEL PEAK 35(16Q21) WILD-TYPE                                30
D86V3, multiclass
                                         clus
vv                                        DEL PEAK 35(16Q21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         59
  MIXED SEROUS AND ENDOMETRIOID                                    8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               74
                                         clus
vv                                        DEL PEAK 35(16Q21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          321
  MIXED SEROUS AND ENDOMETRIOID                                     13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V4, binary
                              cls
clus                             0   1
  DEL PEAK 35(16Q21) MUTATED    32 109
  DEL PEAK 35(16Q21) WILD-TYPE 106 258
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(16Q21) MUTATED     32  109
  DEL PEAK 35(16Q21) WILD-TYPE  106  258
     clus
vv    DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE
  NO                          32                          106
  YES                        109                          258
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 35(16Q21) MUTATED    92   8   8   8
  DEL PEAK 35(16Q21) WILD-TYPE 259  14   9  22
D86V5, multiclass
    clus
vv   DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE
  R0                         92                          259
  R1                          8                           14
  R2                          8                            9
  RX                          8                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(16Q21) MUTATED                                  1     2
  DEL PEAK 35(16Q21) WILD-TYPE                                3    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(16Q21) MUTATED                          36
  DEL PEAK 35(16Q21) WILD-TYPE                        54
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 35(16Q21) MUTATED                                           2    90
  DEL PEAK 35(16Q21) WILD-TYPE                                         7   267
D86V6, multiclass
                                           clus
vv                                          DEL PEAK 35(16Q21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         36
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             90
                                           clus
vv                                          DEL PEAK 35(16Q21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           54
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  WHITE                                                              267
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D86V7, binary
                              cls
clus                             0   1
  DEL PEAK 35(16Q21) MUTATED     3  99
  DEL PEAK 35(16Q21) WILD-TYPE  10 251
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(16Q21) MUTATED      3   99
  DEL PEAK 35(16Q21) WILD-TYPE   10  251
                        clus
vv                       DEL PEAK 35(16Q21) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         99
                        clus
vv                       DEL PEAK 35(16Q21) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          251
[1] 2 2
[1] FALSE

Clustering(87) Variable = DEL PEAK 36(16Q22.3) MUTATION ANALYSIS
D87V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16Q22.3) MUTATED   122  21
  DEL PEAK 36(16Q22.3) WILD-TYPE 321  39
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                           143                            360 
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                            21                             39 
$`DEL PEAK 36(16Q22.3) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       37.02        87.32        65.75        60.53        36.82        19.96 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       17.59        11.44        91.04        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF 
        1.18         1.08         0.39         0.85         0.49         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU 
        2.24        22.26         1.35         0.76         1.71         0.99 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF 
       21.99        39.42        57.80        36.89        48.79         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06B 
       97.71        41.95         0.56        29.69        72.03        53.92 
TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       28.54        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 
       76.83        72.56        25.12        36.39        11.08        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO 
       71.24        61.18        40.50        19.36         2.96        38.70 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K6 TCGA-B5-A0KB TCGA-B5-A11G 
        0.23         0.13        43.13        13.74         4.11       113.36 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD 
       75.72        36.82       102.31        11.87        12.79        33.11 
TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VW 
       34.95         7.92        36.49        20.28        24.39        16.34 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CC TCGA-BK-A26L 
       12.56        13.78        15.45        23.70        10.22        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16G TCGA-D1-A16I 
       16.64        61.87        49.55        22.55        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17M 
       29.92        31.07        18.67         6.77        28.08        10.22 
TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG 
       11.15        13.22         0.72        18.25         2.07         4.27 
TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        4.11        35.38         9.37        31.10        91.96        48.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ 
       10.92        37.71        32.38        19.40        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GK TCGA-EY-A1GM 
       26.96        22.26        16.34         4.54        22.78         6.90 
TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3L3 
       17.62        15.81        12.59        14.40        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EU 
       13.84        17.92         3.72         5.88        34.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.07        28.93        25.02        26.01        41.06 
TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       45.01         2.43        23.97        12.92         7.00 

$`DEL PEAK 36(16Q22.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP 
        3.22       105.37        74.10        57.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       38.37        28.27        20.81        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         7.92        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O 
        9.60         8.02        46.32         5.33         5.16         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       19.79         2.40         3.02         0.76         1.68         1.64 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49         1.28         0.92        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87        16.87         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
        8.22        45.53         7.86        12.20        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        63.16        36.36        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W 
       16.24        18.25        33.73        13.58        19.82        68.35 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D 
       46.45        35.34        45.99        66.58        34.98        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW 
       51.09        27.39        30.02        60.66        35.01        37.78 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CE 
       43.82        40.11        65.88        13.28        19.20        20.05 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       54.12        67.50         4.77        33.53        68.71        33.40 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        27.32        31.13         0.23         0.10 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18         8.35        14.47        80.38        56.91        46.75 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        23.01        17.88        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       11.01         8.71       185.79        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        14.40        14.70        11.70        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        78.81        62.14         5.03        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        34.98 
TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY 
       43.30        43.04        39.32        30.81        21.17        15.42 
TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        34.29        52.64        52.83        56.58        14.83 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       35.67        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
        6.21        10.16        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        23.47        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        67.20 
TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT TCGA-BS-A0UV 
       88.34        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        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         1.41         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-A17N 
        0.99        30.44         1.28        28.01        26.37         1.51 
TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY 
        1.78        24.30         2.33        22.92         1.41        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        8.48        44.88         0.26        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        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        6.67        24.33        16.01         7.36        16.80        18.81 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       19.36        35.15        12.89         6.21        14.99         8.15 
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        13.97 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        15.09        16.11        12.43 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
        8.55         6.48        19.33         3.62        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       13.45        45.76        31.04         6.44         2.14         6.97 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.29        40.01        33.99        36.00         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB 
        8.98        28.96         1.74        13.15        10.82         9.11 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                        113.36                         191.84 
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                         19.96                          23.47 
[1] "0.0 - 113.4 (20.0)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.6"
D87V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 36(16Q22.3) MUTATED                                        63
  DEL PEAK 36(16Q22.3) WILD-TYPE                                     317
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 36(16Q22.3) MUTATED                               8
  DEL PEAK 36(16Q22.3) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 36(16Q22.3) MUTATED                                  73
  DEL PEAK 36(16Q22.3) WILD-TYPE                                31
D87V3, multiclass
                                         clus
vv                                        DEL PEAK 36(16Q22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           63
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 73
                                         clus
vv                                        DEL PEAK 36(16Q22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            317
  MIXED SEROUS AND ENDOMETRIOID                                       13
  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"
D87V4, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q22.3) MUTATED    34 110
  DEL PEAK 36(16Q22.3) WILD-TYPE 104 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q22.3) MUTATED     34  110
  DEL PEAK 36(16Q22.3) WILD-TYPE  104  257
     clus
vv    DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE
  NO                            34                            104
  YES                          110                            257
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(16Q22.3) MUTATED    95   9   8   9
  DEL PEAK 36(16Q22.3) WILD-TYPE 256  13   9  21
D87V5, multiclass
    clus
vv   DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE
  R0                           95                            256
  R1                            9                             13
  R2                            8                              9
  RX                            9                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(16Q22.3) MUTATED                                  1     2
  DEL PEAK 36(16Q22.3) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(16Q22.3) MUTATED                          36
  DEL PEAK 36(16Q22.3) WILD-TYPE                        54
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 36(16Q22.3) MUTATED                                           2
  DEL PEAK 36(16Q22.3) WILD-TYPE                                         7
                                vv
clus                             WHITE
  DEL PEAK 36(16Q22.3) MUTATED      93
  DEL PEAK 36(16Q22.3) WILD-TYPE   264
D87V6, multiclass
                                           clus
vv                                          DEL PEAK 36(16Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           36
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               93
                                           clus
vv                                          DEL PEAK 36(16Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             54
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                264
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D87V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q22.3) MUTATED     4 103
  DEL PEAK 36(16Q22.3) WILD-TYPE   9 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q22.3) MUTATED      4  103
  DEL PEAK 36(16Q22.3) WILD-TYPE    9  247
                        clus
vv                       DEL PEAK 36(16Q22.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       DEL PEAK 36(16Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            247
[1] 2 2
[1] FALSE

Clustering(88) Variable = DEL PEAK 37(16Q23.1) MUTATION ANALYSIS
D88V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16Q23.1) MUTATED   126  25
  DEL PEAK 37(16Q23.1) WILD-TYPE 317  35
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           151                            352 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            25                             35 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       87.32        65.75        60.53        36.82        19.96        17.59 
TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       11.44        91.04        28.64         7.33        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM 
        1.08         0.39         0.85         0.49         1.12        22.26 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A 
        1.35         0.76         1.71         0.99        21.99        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LI 
       57.80        45.53        36.89        48.79         3.39        97.71 
TCGA-AP-A1DQ TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A0IU 
       41.95        29.69        72.03        53.92        51.09        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       37.78        16.96        13.55        15.25        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 
       76.83        72.56        25.12        36.39         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW 
       71.24        40.50        19.36         2.96        38.70         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.13         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K6 TCGA-B5-A0KB TCGA-B5-A11G 
        0.13        43.13        23.01        13.74         4.11       113.36 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD 
       75.72        36.82       102.31        11.87        12.79        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MU TCGA-BG-A0VT 
        5.03        34.95         7.92        36.49        20.28        24.39 
TCGA-BG-A0VW TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0CC 
       16.34        12.56        13.78        15.45        23.70        10.22 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       24.13        16.64         4.80        61.87        49.55        22.55 
TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 
       39.48        27.42        29.92        31.07        18.67         6.77 
TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
       28.08        10.22        11.15        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO 
       16.87         2.07         4.27         4.11        35.38         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       31.10        91.96        48.36        24.33        10.92        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       32.38        19.40        34.39        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       16.34         4.54        22.78         6.90        17.62        15.09 
TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       15.81        12.59        14.40        13.45        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CY 
       13.84         6.44        17.92         3.72         5.88        34.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01         9.07        28.93        25.02        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A7D5 TCGA-PG-A914 
       41.06        45.01         1.74         2.43        23.97        12.92 
TCGA-PG-A915 
        7.00 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
       32.78         3.22       105.37        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        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         7.92 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
       36.33         9.60         8.02        46.32         5.33         5.16 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI 
        1.97        19.79         2.40         3.02         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        1.68         1.64        14.66        22.49         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       36.99        20.65        15.62         1.94        15.95         1.87 
TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       16.87         2.33         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       23.31        86.07         8.22         7.86        12.20        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        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        18.25        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       19.82        68.35        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       34.98        12.26        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CE 
       43.82        40.11        65.88        13.28        19.20        20.05 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       54.12        67.50        11.08        33.53        61.18        68.71 
TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       33.40        26.33        17.75        27.32        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR 
        0.10         1.18         8.35        14.47        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K7 TCGA-B5-A0K8 
       28.34        30.51        25.91        17.88        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       11.01         8.71       185.79        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
       50.89        14.40        14.70        11.70        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       96.30        78.81        62.14        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        34.98        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0VV 
       43.04        39.32        30.81        21.17        15.42        26.66 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 
       34.29        52.64        52.83        56.58        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.16        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        23.47        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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP 
       63.58        63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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-A16I TCGA-D1-A16O TCGA-D1-A16Q 
       36.36        37.51        36.79        11.51        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         1.41         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-A17N TCGA-D1-A17Q TCGA-D1-A17S 
        1.28        28.01        26.37         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        2.33        22.92         1.41        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
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        17.06         2.37         6.67        16.01         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        18.81        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EY-A1G7 
       57.60        24.79        19.36        35.15        12.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT 
       23.90        13.97        19.27        18.84        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 
       12.43         8.55         6.48        19.33         3.62        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       22.82        45.76        31.04         2.14         6.97         5.29 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        33.99        36.00         7.99        13.84         8.98 
TCGA-FI-A2F4 TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       28.96        13.15        10.82         9.11        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        113.36                         191.84 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        19.960                         23.685 
[1] "0.0 - 113.4 (20.0)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2"  
D88V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                        65
  DEL PEAK 37(16Q23.1) WILD-TYPE                                     315
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 37(16Q23.1) MUTATED                               7
  DEL PEAK 37(16Q23.1) WILD-TYPE                            14
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                  80
  DEL PEAK 37(16Q23.1) WILD-TYPE                                24
D88V3, multiclass
                                         clus
vv                                        DEL PEAK 37(16Q23.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           65
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 80
                                         clus
vv                                        DEL PEAK 37(16Q23.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            315
  MIXED SEROUS AND ENDOMETRIOID                                       14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    36 116
  DEL PEAK 37(16Q23.1) WILD-TYPE 102 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     36  116
  DEL PEAK 37(16Q23.1) WILD-TYPE  102  251
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                            36                            102
  YES                          116                            251
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(16Q23.1) MUTATED    98   8  11  10
  DEL PEAK 37(16Q23.1) WILD-TYPE 253  14   6  20
D88V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  R0                           98                            253
  R1                            8                             14
  R2                           11                              6
  RX                           10                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(16Q23.1) MUTATED                                  1     3
  DEL PEAK 37(16Q23.1) WILD-TYPE                                3    16
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(16Q23.1) MUTATED                          42
  DEL PEAK 37(16Q23.1) WILD-TYPE                        48
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 37(16Q23.1) MUTATED                                           2
  DEL PEAK 37(16Q23.1) WILD-TYPE                                         7
                                vv
clus                             WHITE
  DEL PEAK 37(16Q23.1) MUTATED      94
  DEL PEAK 37(16Q23.1) WILD-TYPE   263
D88V6, multiclass
                                           clus
vv                                          DEL PEAK 37(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                           42
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               94
                                           clus
vv                                          DEL PEAK 37(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 16
  BLACK OR AFRICAN AMERICAN                                             48
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                263
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED     4 109
  DEL PEAK 37(16Q23.1) WILD-TYPE   9 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      4  109
  DEL PEAK 37(16Q23.1) WILD-TYPE    9  241
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            241
[1] 2 2
[1] FALSE

Clustering(89) Variable = DEL PEAK 38(17P13.3) MUTATION ANALYSIS
D89V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(17P13.3) MUTATED    88  21
  DEL PEAK 38(17P13.3) WILD-TYPE 355  39
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                           109                            394 
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                            21                             39 
$`DEL PEAK 38(17P13.3) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        19.96        11.44        28.64         7.33 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        1.08         0.39         0.49         1.12         2.24         1.64 
TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
        1.28         0.76        16.87         1.71         0.99        21.99 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH 
        5.95        57.80        45.53        48.79       125.42        36.36 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IU 
       41.95        18.25        33.73         0.56        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CR TCGA-AX-A2H8 TCGA-AX-A2HF 
       37.78        16.96        13.55        11.08        61.18        19.36 
TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       17.75        38.70         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 
        0.03         0.13         0.13        80.38        23.01        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 
        4.11        75.72        43.96       102.31        11.87        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C 
      116.25        33.11         5.03         7.92        36.49        15.45 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
        6.81        10.16        24.13        16.64        61.87        67.20 
TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N 
       49.55        29.95        22.55        39.48        37.32        31.07 
TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU 
       18.67        13.22         0.72        35.38         9.37        31.10 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       24.33        10.92        18.81        37.71        32.38        19.40 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS 
       22.26        16.34        23.90         6.90        17.62        15.09 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A 
        8.55         3.62        29.10         6.44        17.92         3.72 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       34.98        36.00        28.93        25.02        41.06        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
        1.74        13.15         2.43        10.82        23.97         7.00 
TCGA-PG-A917 
        6.97 

$`DEL PEAK 38(17P13.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M 
       91.04        46.32         5.33         5.16        14.96         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        1.97        19.79         0.85         2.40         3.02         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC 
        1.68        14.66        22.49        22.26         0.92        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65         1.35        15.62         1.94        15.95         1.87 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        2.33         2.70         0.13        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        39.42        36.89         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        97.71        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       27.85        16.24        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39         4.77        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       33.53        68.71        33.40        40.50        26.33        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G7 TCGA-AX-A3G8 
        2.96        31.13         0.23         0.10         0.23         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       25.91        17.88        13.74        17.10        11.01         8.71 
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        45.90        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       14.40        14.70        11.70        15.29        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        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        34.98        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
       11.31        35.90        34.98         6.21        10.22        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        23.47 
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        88.34        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        62.79        63.58        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79         8.55         0.56         4.87 
TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W 
       28.67        23.93         1.74         4.44        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         1.41 
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 
        6.77         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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.52        41.42         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.11        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        6.67        16.01         7.36        16.80        31.96        35.05 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU 
       33.01        27.12        57.60        24.79        34.39        19.36 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 
       35.15        12.89        27.16        26.96         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT 
       22.78        13.97        19.27        18.84        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        13.45        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       13.84         2.14         6.97         5.29         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       33.99         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
        9.07        28.96        26.01         9.11        12.92        11.24 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                        18.250                         23.815 
[1] "0.0 - 125.4 (18.2)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2.3"
D89V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 38(17P13.3) MUTATED                                        42
  DEL PEAK 38(17P13.3) WILD-TYPE                                     338
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 38(17P13.3) MUTATED                               9
  DEL PEAK 38(17P13.3) WILD-TYPE                            12
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 38(17P13.3) MUTATED                                  59
  DEL PEAK 38(17P13.3) WILD-TYPE                                45
D89V3, multiclass
                                         clus
vv                                        DEL PEAK 38(17P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           42
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 59
                                         clus
vv                                        DEL PEAK 38(17P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            338
  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"
D89V4, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.3) MUTATED    23  87
  DEL PEAK 38(17P13.3) WILD-TYPE 115 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.3) MUTATED     23   87
  DEL PEAK 38(17P13.3) WILD-TYPE  115  280
     clus
vv    DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE
  NO                            23                            115
  YES                           87                            280
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(17P13.3) MUTATED    68   7   4  10
  DEL PEAK 38(17P13.3) WILD-TYPE 283  15  13  20
D89V5, multiclass
    clus
vv   DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE
  R0                           68                            283
  R1                            7                             15
  R2                            4                             13
  RX                           10                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(17P13.3) MUTATED                                  0     2
  DEL PEAK 38(17P13.3) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(17P13.3) MUTATED                          32
  DEL PEAK 38(17P13.3) WILD-TYPE                        58
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 38(17P13.3) MUTATED                                           3
  DEL PEAK 38(17P13.3) WILD-TYPE                                         6
                                vv
clus                             WHITE
  DEL PEAK 38(17P13.3) MUTATED      66
  DEL PEAK 38(17P13.3) WILD-TYPE   291
D89V6, multiclass
                                           clus
vv                                          DEL PEAK 38(17P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               66
                                           clus
vv                                          DEL PEAK 38(17P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                291
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D89V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.3) MUTATED     3  77
  DEL PEAK 38(17P13.3) WILD-TYPE  10 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.3) MUTATED      3   77
  DEL PEAK 38(17P13.3) WILD-TYPE   10  273
                        clus
vv                       DEL PEAK 38(17P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       DEL PEAK 38(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            273
[1] 2 2
[1] FALSE

Clustering(90) Variable = DEL PEAK 39(17P11.2) MUTATION ANALYSIS
D90V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17P11.2) MUTATED    92  22
  DEL PEAK 39(17P11.2) WILD-TYPE 351  38
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                           114                            389 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            22                             38 
$`DEL PEAK 39(17P11.2) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       65.75        60.53        36.82        19.96        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       91.04        28.64         7.33         1.18         1.08         0.39 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NF 
        1.12         2.24         1.64         1.28         0.92         1.35 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A053 TCGA-AP-A05A 
        0.76        16.87         1.71         0.99         5.95        39.42 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH 
       57.80        45.53        36.89        48.79       125.42        36.36 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       97.71        41.95         0.56        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HF 
       13.55        76.83        11.08         4.77        71.24        19.36 
TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       17.75        38.70         0.33         0.13         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 
        0.03         0.23         1.18         0.13        23.01        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
        4.11        75.72        43.96       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A139 
       12.79       116.25        33.11        36.49        15.45        10.16 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V 
       24.13        16.64        67.20        29.95        22.55        39.48 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW 
       37.32        11.51        31.07        18.67        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU 
       18.25        44.88         4.11        35.38         9.37        31.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       48.36        24.33        10.92        18.81        37.71        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GW 
       19.40        34.39        22.26         6.90        17.62         8.55 
TCGA-EY-A212 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 
        3.62         6.44        17.92         3.72        34.98        36.00 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.07        28.93        25.02        26.01        41.06        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 
        1.74        13.15         2.43        10.82        23.97         7.00 

$`DEL PEAK 39(17P11.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
       15.95         7.92         9.60         8.02        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        5.16        14.96         1.97        19.79         0.85         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        3.02         0.49         0.76         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       22.26        36.99        20.65        15.62         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        1.87         2.33         2.70         0.13        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       23.31        86.07         8.22         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
      117.99       110.37         3.39        63.16        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        18.25        33.73        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        35.01        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       19.20        15.25        20.28        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39        30.12        33.53 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       61.18        68.71        33.40        40.50        26.33        27.32 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G4 TCGA-AX-A3G9 
        2.96        31.13         0.23         0.10         0.13         8.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47        80.38        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       25.91        17.88        13.74        17.10        11.01         8.71 
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        45.90        40.50 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       36.82        32.09        33.50        27.35        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       191.84        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        11.70        15.29        96.30        78.81        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
        5.03        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE 
       15.45        14.27         1.81         9.57        35.67        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
       10.22        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        23.47        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        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-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         1.41         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         6.77         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-A1O0 TCGA-D1-A1O5 
       22.92         1.41        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
        1.05         3.95         3.52        41.42         8.48         0.26 
TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
        4.27        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        91.96        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.01         7.36        16.80        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       27.12        57.60        24.79        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        26.96        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       22.78        13.97        19.27        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        15.81         6.48        19.33        12.59 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        13.45        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       29.10        27.35        13.84         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.88        40.01        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
       96.69        59.01        28.96         9.11        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        6.97        18.84        39.95         4.21         5.52 

  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                         18.74                          23.47 
[1] "0.0 - 125.4 (18.7)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.3"
D90V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 39(17P11.2) MUTATED                                        41
  DEL PEAK 39(17P11.2) WILD-TYPE                                     339
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 39(17P11.2) MUTATED                               8
  DEL PEAK 39(17P11.2) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 39(17P11.2) MUTATED                                  66
  DEL PEAK 39(17P11.2) WILD-TYPE                                38
D90V3, multiclass
                                         clus
vv                                        DEL PEAK 39(17P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           41
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 66
                                         clus
vv                                        DEL PEAK 39(17P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            339
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V4, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED    25  90
  DEL PEAK 39(17P11.2) WILD-TYPE 113 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     25   90
  DEL PEAK 39(17P11.2) WILD-TYPE  113  277
     clus
vv    DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  NO                            25                            113
  YES                           90                            277
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17P11.2) MUTATED    73   7   4   8
  DEL PEAK 39(17P11.2) WILD-TYPE 278  15  13  22
D90V5, multiclass
    clus
vv   DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  R0                           73                            278
  R1                            7                             15
  R2                            4                             13
  RX                            8                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(17P11.2) MUTATED                                  0     2
  DEL PEAK 39(17P11.2) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(17P11.2) MUTATED                          31
  DEL PEAK 39(17P11.2) WILD-TYPE                        59
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 39(17P11.2) MUTATED                                           1
  DEL PEAK 39(17P11.2) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK 39(17P11.2) MUTATED      74
  DEL PEAK 39(17P11.2) WILD-TYPE   283
D90V6, multiclass
                                           clus
vv                                          DEL PEAK 39(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               74
                                           clus
vv                                          DEL PEAK 39(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             59
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                283
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D90V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED     3  79
  DEL PEAK 39(17P11.2) WILD-TYPE  10 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED      3   79
  DEL PEAK 39(17P11.2) WILD-TYPE   10  271
                        clus
vv                       DEL PEAK 39(17P11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 39(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            271
[1] 2 2
[1] FALSE

Clustering(91) Variable = DEL PEAK 40(17Q11.2) MUTATION ANALYSIS
D91V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17Q11.2) MUTATED    78  16
  DEL PEAK 40(17Q11.2) WILD-TYPE 365  44
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            94                            409 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            16                             44 
$`DEL PEAK 40(17Q11.2) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       65.75        60.53        19.96        17.59        11.44        36.33 
TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BI 
        7.33         1.18         1.08         0.39         0.85         2.24 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A052 
       22.26         1.28         0.92         0.76         1.71        21.99 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       39.42        57.80        45.53        48.79       125.42        97.71 
TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A1CR 
       41.95         0.56        37.78        13.55        76.83        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2IO TCGA-AX-A3FW 
       30.12        71.24        61.18        19.36        38.70         0.33 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-B5-A11N 
        0.13         0.20        20.52         0.03         0.23        43.96 
TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0M6 
      102.31        12.79       116.25        33.11        34.13         7.92 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       36.49        15.45         6.81        10.16        24.13        16.64 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
       61.87        67.20        49.55        22.55        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 
       31.07         6.77        28.08        13.22         0.72         2.07 
TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EC-A24G 
        4.11         9.37        31.10        48.36        24.33        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3KU 
       18.81        37.71        32.38        19.40        34.39        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2OQ 
       16.34         4.54        23.90         8.55         3.62        29.10 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F8 
       13.84        17.92        34.98        36.00        59.01        25.02 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A7D5 TCGA-PG-A914 
       26.01         1.74        23.97        12.92 

$`DEL PEAK 40(17Q11.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
       15.95         7.92         9.60         8.02        91.04        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL 
       28.64         5.33         5.16        14.96         1.97        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40         3.02         0.49         1.12         0.76         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
        1.64        14.66        22.49        36.99        20.65         1.35 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87        16.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
        0.99         2.70         0.13        83.67         5.95        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        36.89         7.86        12.20        20.91 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        18.25        33.73        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        13.28        19.20        16.96        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39         4.77        33.53        68.71        33.40        40.50 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       26.33        17.75        27.32         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.10         0.13         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       23.01        17.88        13.74        17.10        17.85        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
        4.11         8.71       185.79       113.36        88.34        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        40.50        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84        50.89        14.40        14.70        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3S1 
       11.87        15.29        96.30        78.81        62.14         5.03 
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        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        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         6.21        10.22        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        23.47        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 
       88.34        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        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93         1.74         4.44        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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        36.10        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         1.41 
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-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-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30        35.38        12.39        91.96        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EO-A1Y5 
       17.06         2.37         6.67        16.01         7.36        10.92 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       31.96        35.05        33.01        27.12        57.60        24.79 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 
       19.36        35.15        12.89        27.16        26.96         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        12.59        14.40        18.87        22.82        13.45 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04        27.35         6.44         2.14         6.97 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 
        3.72         5.29         5.88        40.01        33.99         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 
       13.84         8.98        96.69         9.07        28.93        28.96 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       41.06        45.01        13.15         2.43        10.82         9.11 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                        21.255                         23.310 
[1] "0.0 - 125.4 (21.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.7"
D91V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 40(17Q11.2) MUTATED                                        42
  DEL PEAK 40(17Q11.2) WILD-TYPE                                     338
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 40(17Q11.2) MUTATED                               5
  DEL PEAK 40(17Q11.2) WILD-TYPE                            16
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 40(17Q11.2) MUTATED                                  48
  DEL PEAK 40(17Q11.2) WILD-TYPE                                56
D91V3, multiclass
                                         clus
vv                                        DEL PEAK 40(17Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           42
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 48
                                         clus
vv                                        DEL PEAK 40(17Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            338
  MIXED SEROUS AND ENDOMETRIOID                                       16
  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"
D91V4, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED    20  75
  DEL PEAK 40(17Q11.2) WILD-TYPE 118 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED     20   75
  DEL PEAK 40(17Q11.2) WILD-TYPE  118  292
     clus
vv    DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  NO                            20                            118
  YES                           75                            292
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17Q11.2) MUTATED    62   6   6   6
  DEL PEAK 40(17Q11.2) WILD-TYPE 289  16  11  24
D91V5, multiclass
    clus
vv   DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  R0                           62                            289
  R1                            6                             16
  R2                            6                             11
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(17Q11.2) MUTATED                                  0     2
  DEL PEAK 40(17Q11.2) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(17Q11.2) MUTATED                          19
  DEL PEAK 40(17Q11.2) WILD-TYPE                        71
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 40(17Q11.2) MUTATED                                           2
  DEL PEAK 40(17Q11.2) WILD-TYPE                                         7
                                vv
clus                             WHITE
  DEL PEAK 40(17Q11.2) MUTATED      65
  DEL PEAK 40(17Q11.2) WILD-TYPE   292
D91V6, multiclass
                                           clus
vv                                          DEL PEAK 40(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               65
                                           clus
vv                                          DEL PEAK 40(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                292
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D91V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED     3  65
  DEL PEAK 40(17Q11.2) WILD-TYPE  10 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED      3   65
  DEL PEAK 40(17Q11.2) WILD-TYPE   10  285
                        clus
vv                       DEL PEAK 40(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           65
                        clus
vv                       DEL PEAK 40(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            285
[1] 2 2
[1] FALSE

Clustering(92) Variable = DEL PEAK 41(17Q21.31) MUTATION ANALYSIS
D92V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 41(17Q21.31) MUTATED    80  20
  DEL PEAK 41(17Q21.31) WILD-TYPE 363  40
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                            100                             403 
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                             20                              40 
$`DEL PEAK 41(17Q21.31) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A3LO 
       65.75        60.53        17.59        11.44        91.04         7.33 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EM 
        1.18         1.08         0.39         0.85         2.24        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A052 
        1.28         0.92         1.35         0.76         1.71        21.99 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
        5.95        39.42        57.80        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A1C7 
      125.42        97.71        41.95        33.73         0.56        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2IO 
       13.55        36.39        30.12        71.24        61.18        38.70 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.33         0.13         0.20        20.52         0.03         0.13 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A3F9 
       23.01        17.85         4.11        43.96       102.31       116.25 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C 
       33.11         5.03        34.13         7.92        36.49        15.45 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 
        6.81        10.22        24.13        16.64        67.20        49.55 
TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 
       29.95        22.55        37.32        11.51        31.07         6.77 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DI-A1NO 
       28.08        13.22        18.25         2.07         4.11         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       12.39        31.10        24.33        18.81        37.71        32.38 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ 
       19.40        34.39        22.26        16.34         4.54        23.90 
TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A4KR 
       17.62         8.55        12.59         3.62        29.10         6.44 
TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F8 
       17.92        34.98        36.00        96.69        28.93        25.02 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-PG-A7D5 TCGA-PG-A914 
        1.74         2.43        23.97        12.92 

$`DEL PEAK 41(17Q21.31) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O 
       46.32        28.64         5.33         5.16        14.96         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         2.40         3.02         0.49         1.12         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68         1.64        14.66        22.49        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW 
       15.62         1.94        15.95         1.87        16.87         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 
        0.99         2.70         0.13        83.67        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
        8.22         7.86        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
        3.39        63.16        36.36        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        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        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       18.25        13.58        19.82        29.69        68.35        72.03 
TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B 
       46.45        35.34        45.99        66.58        34.98        53.92 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       28.54        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       19.20        15.25        20.28        12.43        20.05        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 
       72.56        54.12        67.50        25.12        11.08         4.77 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       33.53        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        27.32         2.96        31.13         0.23         0.10 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23         1.18         8.35        14.47         0.13        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        11.01         8.71       185.79       113.36 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11O TCGA-B5-A11P 
       88.34        75.72        54.44        45.90        40.50        36.82 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA 
       14.70        11.70        11.87        15.29        12.79        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        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        34.98        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        34.29        52.64        52.83        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       14.83        12.56        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.27         1.81         9.57        35.67        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         6.21        10.16        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        23.47 
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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 
        4.87        28.67        23.93         1.74         4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        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         1.41         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-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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ 
       41.42         8.48        44.88         0.26         4.27        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        35.38        91.96 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.01 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        10.92        31.96        35.05        33.01 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       27.12        57.60        24.79        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       27.16        26.96         6.21        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       19.27        18.84        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81         6.48        19.33        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 
       13.45        45.76        31.04        27.35        13.84         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
        6.97         3.72         5.29         5.88        40.01        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
        7.99        13.84         8.98        59.01         9.07        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB 
       26.01        41.06        45.01        13.15        10.82         9.11 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                         125.42                          191.84 
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                         19.105                          23.380 
[1] "0.0 - 125.4 (19.1)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.3"
D92V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 41(17Q21.31) MUTATED                                        41
  DEL PEAK 41(17Q21.31) WILD-TYPE                                     339
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 41(17Q21.31) MUTATED                               5
  DEL PEAK 41(17Q21.31) WILD-TYPE                            16
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 41(17Q21.31) MUTATED                                  54
  DEL PEAK 41(17Q21.31) WILD-TYPE                                50
D92V3, multiclass
                                         clus
vv                                        DEL PEAK 41(17Q21.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            41
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  54
                                         clus
vv                                        DEL PEAK 41(17Q21.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             339
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V4, binary
                                 cls
clus                                0   1
  DEL PEAK 41(17Q21.31) MUTATED    21  79
  DEL PEAK 41(17Q21.31) WILD-TYPE 117 288
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(17Q21.31) MUTATED     21   79
  DEL PEAK 41(17Q21.31) WILD-TYPE  117  288
     clus
vv    DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE
  NO                             21                             117
  YES                            79                             288
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 41(17Q21.31) MUTATED    61   6   6  10
  DEL PEAK 41(17Q21.31) WILD-TYPE 290  16  11  20
D92V5, multiclass
    clus
vv   DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE
  R0                            61                             290
  R1                             6                              16
  R2                             6                              11
  RX                            10                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(17Q21.31) MUTATED                                  1     2
  DEL PEAK 41(17Q21.31) WILD-TYPE                                3    17
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(17Q21.31) MUTATED                          23
  DEL PEAK 41(17Q21.31) WILD-TYPE                        67
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 41(17Q21.31) MUTATED                                           3
  DEL PEAK 41(17Q21.31) WILD-TYPE                                         6
                                 vv
clus                              WHITE
  DEL PEAK 41(17Q21.31) MUTATED      64
  DEL PEAK 41(17Q21.31) WILD-TYPE   293
D92V6, multiclass
                                           clus
vv                                          DEL PEAK 41(17Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                            23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                64
                                           clus
vv                                          DEL PEAK 41(17Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  17
  BLACK OR AFRICAN AMERICAN                                              67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  WHITE                                                                 293
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V7, binary
                                 cls
clus                                0   1
  DEL PEAK 41(17Q21.31) MUTATED     6  65
  DEL PEAK 41(17Q21.31) WILD-TYPE   7 285
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(17Q21.31) MUTATED      6   65
  DEL PEAK 41(17Q21.31) WILD-TYPE    7  285
                        clus
vv                       DEL PEAK 41(17Q21.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            65
                        clus
vv                       DEL PEAK 41(17Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             285
[1] 2 2
[1] FALSE

Clustering(93) Variable = DEL PEAK 42(18Q21.2) MUTATION ANALYSIS
D93V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q21.2) MUTATED    72  10
  DEL PEAK 42(18Q21.2) WILD-TYPE 371  50
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            82                            421 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            10                             50 
$`DEL PEAK 42(18Q21.2) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG 
       37.02        65.75        60.53        36.82        17.59        11.44 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK 
       46.32        28.64         7.33        14.96         1.18         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3NF TCGA-AP-A05H TCGA-AP-A0L9 
        0.85         0.49         1.12         1.35        45.53       125.42 
TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A0IU TCGA-AX-A1CA TCGA-AX-A1CF 
        3.39        36.36        97.71        28.54        20.28        76.83 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       11.08         4.77         2.96         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A11H TCGA-B5-A11P 
        0.13         0.23         0.13        80.38        88.34        36.82 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE 
       12.79       116.25        33.11        34.95        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 
        6.81        10.22        10.16        16.64        67.20        49.55 
TCGA-D1-A0ZP TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW 
       29.95        37.32        18.67         1.41        28.08         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 
        2.07         4.11        31.10        91.96        48.36        18.81 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP 
       37.71        32.38        27.16         4.54        19.27        18.84 
TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3QX 
       15.09         8.55        14.40        13.45        45.76        13.84 
TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX 
       17.92         5.88        34.98         9.07        28.93        45.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 
       13.15         2.43        10.82        23.97 

$`DEL PEAK 42(18Q21.2) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 
        7.92        36.33         9.60         8.02        91.04         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        5.16         1.08         1.97        19.79         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.26         1.28         0.92        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
        0.76         1.94        15.95         1.87        16.87         1.71 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
        2.33         0.99         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
        5.95        23.31        86.07         8.22        39.42        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89         7.86        12.20        20.91        48.79       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
      110.37        63.16        31.73        83.97        27.12        82.52 
TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT TCGA-AP-A0LV 
       33.40        61.64        80.78        63.06        49.22        25.08 
TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        41.95 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       18.25        33.73         0.56        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 
       68.35        72.03        46.45        35.34        45.99        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       34.98        53.92        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       60.66        35.01        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       13.28        19.20        16.96        13.55        15.25        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        72.56        54.12        67.50        25.12        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        33.53        61.18        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       40.50        19.36        26.33        17.75        27.32        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G8 
       38.70         0.23         0.10         0.33         0.13         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        8.35        14.47        56.91        46.75        43.13        48.76 
TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 
       40.67        44.71        32.55        28.64        28.34        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        23.01        17.88        13.74        17.10        17.85 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11I 
       11.01         4.11         8.71       185.79       113.36        75.72 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R 
       54.44        45.90        43.96        40.50        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z 
       27.35        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       191.84       102.31        50.89        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       11.70        11.87        15.29        96.30        78.81        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98         7.92        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK 
       28.27        10.72        41.52        48.56        23.47        43.30 
TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.04        39.32        30.81        21.17        20.28        15.42 
TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       24.39        26.66        16.34        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A 
       56.58        14.83        12.56        13.78        14.73        14.01 
TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 
       15.45        14.27         1.81         9.57        35.67        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         6.21        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        23.47 
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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       63.16        66.48        16.83        19.79         8.55         0.56 
TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 
        4.87        28.67        23.93        22.55         1.74         4.44 
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-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-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02         6.77         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-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22        18.25        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
        0.26         4.27        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 
       24.30        35.38         9.37        12.39        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        24.33        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        22.26        16.34         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        17.88        17.62        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
       15.81         6.48        19.33        12.59         3.62        18.87 
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         6.44         2.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
        6.97         3.72         5.29        40.01        33.99        36.00 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69        59.01        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-PG-A6IB TCGA-PG-A914 
       25.02        26.01        41.06         1.74         9.11        12.92 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                        18.295                         23.340 
[1] "0.0 - 125.4 (18.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.2"
D93V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                                        35
  DEL PEAK 42(18Q21.2) WILD-TYPE                                     345
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 42(18Q21.2) MUTATED                               6
  DEL PEAK 42(18Q21.2) WILD-TYPE                            15
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                                  41
  DEL PEAK 42(18Q21.2) WILD-TYPE                                63
D93V3, multiclass
                                         clus
vv                                        DEL PEAK 42(18Q21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           35
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 41
                                         clus
vv                                        DEL PEAK 42(18Q21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            345
  MIXED SEROUS AND ENDOMETRIOID                                       15
  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"
D93V4, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED    13  69
  DEL PEAK 42(18Q21.2) WILD-TYPE 125 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     13   69
  DEL PEAK 42(18Q21.2) WILD-TYPE  125  298
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  NO                            13                            125
  YES                           69                            298
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q21.2) MUTATED    48   5   5   6
  DEL PEAK 42(18Q21.2) WILD-TYPE 303  17  12  24
D93V5, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  R0                           48                            303
  R1                            5                             17
  R2                            5                             12
  RX                            6                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(18Q21.2) MUTATED                                  0     2
  DEL PEAK 42(18Q21.2) WILD-TYPE                                4    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(18Q21.2) MUTATED                          23
  DEL PEAK 42(18Q21.2) WILD-TYPE                        67
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 42(18Q21.2) MUTATED                                           3
  DEL PEAK 42(18Q21.2) WILD-TYPE                                         6
                                vv
clus                             WHITE
  DEL PEAK 42(18Q21.2) MUTATED      51
  DEL PEAK 42(18Q21.2) WILD-TYPE   306
D93V6, multiclass
                                           clus
vv                                          DEL PEAK 42(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               51
                                           clus
vv                                          DEL PEAK 42(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D93V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED     4  59
  DEL PEAK 42(18Q21.2) WILD-TYPE   9 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED      4   59
  DEL PEAK 42(18Q21.2) WILD-TYPE    9  291
                        clus
vv                       DEL PEAK 42(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 42(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            291
[1] 2 2
[1] FALSE

Clustering(94) Variable = DEL PEAK 43(18Q23) MUTATION ANALYSIS
D94V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 43(18Q23) MUTATED    71  16
  DEL PEAK 43(18Q23) WILD-TYPE 372  44
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          87                          416 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          16                           44 
$`DEL PEAK 43(18Q23) MUTATED`
TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       37.02        65.75        60.53        36.82        19.96        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       11.44        36.33        46.32        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3IA 
        1.18         1.08         0.39         0.49         1.12         0.92 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LF TCGA-AP-A0LH 
        1.35         1.71        21.99        45.53         3.39        36.36 
TCGA-AP-A0LI TCGA-AX-A0IU TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       97.71        28.54        20.28        11.08         4.77        30.12 
TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        2.96         0.20        20.52         0.03         0.13         0.23 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JX TCGA-B5-A11E TCGA-B5-A11P TCGA-B5-A1MY 
        0.13        80.38        44.71         8.71        36.82        11.87 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE TCGA-BG-A3PP 
      116.25        33.11        34.95        15.45        23.70         6.81 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       10.22        10.16        16.64        61.87        67.20        49.55 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 
       37.32        18.67         1.41        28.08         0.72         2.07 
TCGA-D1-A3DH TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y7 
        4.11        12.39        31.10        91.96        48.36        18.81 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GS 
       37.71        32.38        27.16         4.54        18.84        15.09 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX 
        8.55         3.62        13.45        45.76        29.10        13.84 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
        5.88        34.98        59.01         9.07        28.93        25.02 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A7D5 
       13.15         2.43        23.97 

$`DEL PEAK 43(18Q23) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
        3.22       105.37        87.32        74.10        57.53        60.53 
TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX 
       46.55        38.37        28.27        20.81        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         7.92 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O 
        9.60         8.02        91.04         5.33         5.16         1.97 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI 
       19.79         0.85         2.40         3.02         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
        1.87        16.87         2.33         0.99         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67         5.95        23.31        86.07         8.22        39.42 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        36.89         7.86        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL 
      125.42       117.99       110.37        63.16        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       27.85        16.24        18.25        33.73         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       45.99        66.58        34.98        53.92        12.26        51.09 
TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ 
       27.39        30.02        60.66        35.01        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        71.24        33.53        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       68.71        33.40        40.50        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       27.32        31.13        38.70         0.23         0.10         0.33 
TCGA-AX-A3FX TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.13         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       43.13        48.76        40.67        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.85        11.01         4.11       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        45.90        43.96        40.50        32.09 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       33.50        27.35        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       191.84       102.31        50.89        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29        12.79        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14         5.03        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       19.33        20.94        35.21        34.98         7.92        38.37 
TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI 
       36.49        28.27        10.72        41.52        48.56        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       43.30        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ 
       15.42        24.39        26.66        16.34        34.29        52.64 
TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.83        56.58        14.83        12.56        13.78        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
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         6.21        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 
       23.47        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        88.34        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        62.79        63.58 
TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       63.16        66.48        16.83        19.79        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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        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-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-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         6.77         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.27        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        35.38         9.37        23.38        17.06 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        24.33        16.01         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        22.26        16.34         6.21        14.99         8.15 
TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       24.36        27.16        23.34        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       13.97         6.90        19.27        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 
       18.87        22.82        31.04        27.35         6.44        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
        2.14         6.97         3.72         5.29        40.01        33.99 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 
       36.00         7.99        13.84         8.98        96.69        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A5BC TCGA-PG-A6IB 
       26.01        41.06        45.01         1.74        10.82         9.11 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                        0.03                         0.10 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                      116.25                       191.84 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                       18.67                        23.36 
[1] "0.0 - 116.2 (18.7)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.1"
D94V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                        34
  DEL PEAK 43(18Q23) WILD-TYPE                                     346
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 43(18Q23) MUTATED                               6
  DEL PEAK 43(18Q23) WILD-TYPE                            15
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                  47
  DEL PEAK 43(18Q23) WILD-TYPE                                57
D94V3, multiclass
                                         clus
vv                                        DEL PEAK 43(18Q23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         34
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               47
                                         clus
vv                                        DEL PEAK 43(18Q23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          346
  MIXED SEROUS AND ENDOMETRIOID                                     15
  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"
D94V4, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED    12  75
  DEL PEAK 43(18Q23) WILD-TYPE 126 292
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED     12   75
  DEL PEAK 43(18Q23) WILD-TYPE  126  292
     clus
vv    DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  NO                          12                          126
  YES                         75                          292
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 43(18Q23) MUTATED    52   5   8   5
  DEL PEAK 43(18Q23) WILD-TYPE 299  17   9  25
D94V5, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  R0                         52                          299
  R1                          5                           17
  R2                          8                            9
  RX                          5                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(18Q23) MUTATED                                  1     2
  DEL PEAK 43(18Q23) WILD-TYPE                                3    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(18Q23) MUTATED                          23
  DEL PEAK 43(18Q23) WILD-TYPE                        67
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 43(18Q23) MUTATED                                           3    54
  DEL PEAK 43(18Q23) WILD-TYPE                                         6   303
D94V6, multiclass
                                           clus
vv                                          DEL PEAK 43(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          3
  WHITE                                                             54
                                           clus
vv                                          DEL PEAK 43(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           67
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            6
  WHITE                                                              303
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V7, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     5  59
  DEL PEAK 43(18Q23) WILD-TYPE   8 291
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      5   59
  DEL PEAK 43(18Q23) WILD-TYPE    8  291
                        clus
vv                       DEL PEAK 43(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         59
                        clus
vv                       DEL PEAK 43(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          291
[1] 2 2
[1] FALSE

Clustering(95) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D95V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.3) MUTATED   110  30
  DEL PEAK 44(19P13.3) WILD-TYPE 333  30
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           140                            363 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            30                             30 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       60.53        36.82        19.96        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       46.32        28.64         7.33        14.96         1.18         1.08 
TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        0.39         0.85         0.49         1.12         1.64        22.26 
TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 
        1.35        16.87         1.71         0.99        21.99         5.95 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
       39.42        57.80        45.53        36.89        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IU 
        3.39        41.95        18.25        33.73        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP 
       37.78        16.96        13.55        20.28        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF 
       11.08         4.77        30.12        71.24        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        2.96        38.70         0.13         0.20        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.13         0.13        80.38        23.01        17.85         4.11 
TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 
       75.72        36.82       102.31        50.89        11.87        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
      116.25        33.11         5.03        34.13        34.95         7.92 
TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC 
       36.49        21.17        12.56        15.45         6.81        10.22 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V 
       24.13        67.20        49.55        29.95        22.55        39.48 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K 
       27.42        11.51        31.07        18.67         6.77        28.08 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG 
       13.22         0.72        18.25         2.07        44.88         4.27 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        91.96        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU 
       24.33        10.92        37.71        32.38        19.40        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       16.34         4.54        23.90        18.84        17.62        15.09 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 
       15.81         8.55         3.62        14.40        13.45        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       13.84         6.44         3.72        34.98        36.00        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       59.01         9.07        28.93        25.02        26.01        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 
       45.01         1.74        13.15         2.43        10.82        23.97 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        38.37        28.27        20.81 
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-A1OK TCGA-A5-A2K5 
       42.35        15.95         7.92         9.60         8.02         5.33 
TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        5.16         1.97        19.79         2.40         3.02         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
        2.24         1.68        14.66        22.49         1.28         0.92 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        15.62         0.76         1.94        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
        1.87         2.33         2.70         0.13        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       86.07         8.22         7.86        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37        63.16        36.36        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        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        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       12.26        51.09        27.39        30.02        60.66        35.01 
TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 
       43.82        40.11        65.88        13.28        19.20        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       33.53        68.71        33.40        40.50        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G7 
       27.32        31.13         0.23         0.10         0.33         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18         8.35        14.47        56.91        46.75        43.13 
TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 
       48.76        40.67        44.71        32.55        28.64        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       30.51        25.91        17.88        13.74        17.10        11.01 
TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        88.34        54.44        45.90 
TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       43.96        40.50        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB 
       14.40        14.70        11.70        15.29        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       62.14        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        34.98        38.37        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       20.28        15.42        24.39        26.66        16.34        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        35.67 
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         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 
       10.16        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        23.47        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 
       88.34        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        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79         8.55         0.56         4.87        28.67        23.93 
TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74         4.44        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-A16O 
       37.32        36.36        37.51        36.79        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         1.41         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-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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
       41.42         8.48         0.26         4.11        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       39.29        36.62        24.30        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
        6.67        16.01         7.36        16.80        18.81        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       35.05        33.01        27.12        57.60        24.79        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1G7 
       19.36        35.15        12.89        27.16        26.96         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GT 
       22.78        13.97         6.90        19.27        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM 
       12.43         6.48        19.33        12.59        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04        29.10        17.92         2.14         6.97 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.29         5.88        40.01        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        8.98        28.96         9.11        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        125.42                         191.84 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         19.68                          23.47 
[1] "0.0 - 125.4 (19.7)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.9"
D95V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                        41
  DEL PEAK 44(19P13.3) WILD-TYPE                                     339
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 44(19P13.3) MUTATED                               8
  DEL PEAK 44(19P13.3) WILD-TYPE                            13
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                  92
  DEL PEAK 44(19P13.3) WILD-TYPE                                12
D95V3, multiclass
                                         clus
vv                                        DEL PEAK 44(19P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           41
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 92
                                         clus
vv                                        DEL PEAK 44(19P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            339
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V4, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    31 110
  DEL PEAK 44(19P13.3) WILD-TYPE 107 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     31  110
  DEL PEAK 44(19P13.3) WILD-TYPE  107  257
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                            31                            107
  YES                          110                            257
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED    85   9   9  13
  DEL PEAK 44(19P13.3) WILD-TYPE 266  13   8  17
D95V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                           85                            266
  R1                            9                             13
  R2                            9                              8
  RX                           13                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(19P13.3) MUTATED                                  1     2
  DEL PEAK 44(19P13.3) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(19P13.3) MUTATED                          41
  DEL PEAK 44(19P13.3) WILD-TYPE                        49
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 44(19P13.3) MUTATED                                           3
  DEL PEAK 44(19P13.3) WILD-TYPE                                         6
                                vv
clus                             WHITE
  DEL PEAK 44(19P13.3) MUTATED      87
  DEL PEAK 44(19P13.3) WILD-TYPE   270
D95V6, multiclass
                                           clus
vv                                          DEL PEAK 44(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           41
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               87
                                           clus
vv                                          DEL PEAK 44(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             49
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                270
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D95V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     6  96
  DEL PEAK 44(19P13.3) WILD-TYPE   7 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      6   96
  DEL PEAK 44(19P13.3) WILD-TYPE    7  254
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           96
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            254
[1] 2 2
[1] FALSE

Clustering(96) Variable = DEL PEAK 45(19P12) MUTATION ANALYSIS
D96V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 45(19P12) MUTATED    41  11
  DEL PEAK 45(19P12) WILD-TYPE 402  49
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          52                          451 
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          11                           49 
$`DEL PEAK 45(19P12) MUTATED`
TCGA-A5-A0GN TCGA-A5-A3LO TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF 
       60.53         7.33         0.85         0.49         1.64         1.35 
TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1C7 TCGA-AX-A1CA 
        1.71        57.80        18.25        33.73        16.96        20.28 
TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G7 
       76.83         4.77        71.24         2.96         0.20         0.23 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JZ TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU 
        0.13        80.38        28.64        36.82       102.31        50.89 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0YV 
      116.25        33.11        34.13        34.95         7.92        12.56 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16N TCGA-DI-A2QT 
       15.45         6.81        61.87        67.20        31.07        12.39 
TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A214 
       18.81        32.38        26.96        15.81         8.55        14.40 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D2 
       29.10         6.44         3.72         5.88        34.98        36.00 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-PG-A7D5 TCGA-PG-A914 
        9.07        28.93        23.97        12.92 

$`DEL PEAK 45(19P12) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU 
       65.75        60.53        46.55        38.37        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 
       20.81        23.21        68.65        19.96        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         7.92        11.44 
TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       36.33         9.60         8.02        91.04        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O 
        5.33         5.16        14.96         1.18         1.08         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
        0.39        19.79         2.40         3.02         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        2.24         1.68        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
        0.92        36.99        20.65        15.62         0.76         1.94 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95         1.87        16.87         2.33         0.99         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        0.13        83.67        21.99         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        39.42        45.53        36.89         7.86        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       20.91        48.79       125.42       117.99       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
       63.16        36.36        97.71        31.73        83.97        27.12 
TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS TCGA-AP-A0LT 
       82.52        33.40        61.64        80.78        63.06        49.22 
TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP 
       25.08        71.67        60.36        55.89        31.30        35.54 
TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       41.95        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A1E4 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24         0.56        13.58        19.82        29.69        68.35 
TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       72.03        46.45        35.34        45.99        66.58        34.98 
TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       53.92        12.26        51.09        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 
       35.01        28.54        37.78        43.82        40.11        65.88 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        13.55        15.25        12.43        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.23         0.10         0.33         0.13        20.52         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.13         1.18         8.35        14.47        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0K0 
       43.13        48.76        40.67        44.71        32.55        28.34 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 
       30.51        25.91        23.01        17.88        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.85        11.01         4.11         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84        14.40        14.70 
TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        11.87        15.29        12.79        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       62.14         5.03        41.06        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 
       14.83        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        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         6.21        10.22        10.16        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        23.47        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        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        11.51        29.92        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         1.41         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         6.77         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-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
        8.48        44.88         0.26         4.27         4.11        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-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10        91.96        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        24.33        16.01         7.36        16.80        10.92 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       24.79        19.40        34.39        19.36        35.15        12.89 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        22.26        16.34         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
        8.15        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 
       17.62        15.09        16.11        12.43         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       12.59         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       31.04        27.35        13.84        17.92         2.14         6.97 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.29        40.01        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       96.69        59.01        28.96        25.02        26.01        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A6IB 
       45.01         1.74        13.15         2.43        10.82         9.11 
TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
        7.00        11.24         6.97        18.84        39.95         4.21 
TCGA-QS-A5YR 
        5.52 

  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                        0.13                         0.03 
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                      116.25                       191.84 
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                       18.53                        23.01 
[1] "0.1 - 116.2 (18.5)" "0.0 - 191.8 (23.0)"
[1] "hr=" "2.1"
D96V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 45(19P12) MUTATED                                        19
  DEL PEAK 45(19P12) WILD-TYPE                                     361
                              vv
clus                           MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 45(19P12) MUTATED                               5
  DEL PEAK 45(19P12) WILD-TYPE                            16
                              vv
clus                           SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 45(19P12) MUTATED                                  28
  DEL PEAK 45(19P12) WILD-TYPE                                76
D96V3, multiclass
                                         clus
vv                                        DEL PEAK 45(19P12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         19
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               28
                                         clus
vv                                        DEL PEAK 45(19P12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          361
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V4, binary
                              cls
clus                             0   1
  DEL PEAK 45(19P12) MUTATED     8  44
  DEL PEAK 45(19P12) WILD-TYPE 130 323
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19P12) MUTATED      8   44
  DEL PEAK 45(19P12) WILD-TYPE  130  323
     clus
vv    DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE
  NO                           8                          130
  YES                         44                          323
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 45(19P12) MUTATED    29   3   2   6
  DEL PEAK 45(19P12) WILD-TYPE 322  19  15  24
D96V5, multiclass
    clus
vv   DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE
  R0                         29                          322
  R1                          3                           19
  R2                          2                           15
  RX                          6                           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"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(19P12) MUTATED                                  1     1
  DEL PEAK 45(19P12) WILD-TYPE                                3    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(19P12) MUTATED                          16
  DEL PEAK 45(19P12) WILD-TYPE                        74
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 45(19P12) MUTATED                                           1    31
  DEL PEAK 45(19P12) WILD-TYPE                                         8   326
D96V6, multiclass
                                           clus
vv                                          DEL PEAK 45(19P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              1
  BLACK OR AFRICAN AMERICAN                                         16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             31
                                           clus
vv                                          DEL PEAK 45(19P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           74
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            8
  WHITE                                                              326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D96V7, binary
                              cls
clus                             0   1
  DEL PEAK 45(19P12) MUTATED     2  36
  DEL PEAK 45(19P12) WILD-TYPE  11 314
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19P12) MUTATED      2   36
  DEL PEAK 45(19P12) WILD-TYPE   11  314
                        clus
vv                       DEL PEAK 45(19P12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         36
                        clus
vv                       DEL PEAK 45(19P12) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          314
[1] 2 2
[1] FALSE

Clustering(97) Variable = DEL PEAK 46(19Q13.43) MUTATION ANALYSIS
D97V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(19Q13.43) MUTATED    42  15
  DEL PEAK 46(19Q13.43) WILD-TYPE 401  45
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             57                             446 
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             15                              45 
$`DEL PEAK 46(19Q13.43) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO 
       65.75        60.53        19.96        91.04        28.64         7.33 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A6NU 
        1.18         1.08         2.24         0.92         1.35         0.99 
TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       21.99        39.42        57.80        45.53        48.79       125.42 
TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A1CP 
       36.36        18.25        37.78        13.55        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G3 
       11.08         4.77        71.24         2.96         0.20         0.03 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
        0.13         0.23        36.82       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         6.81        10.22        27.42        11.51 
TCGA-D1-A3DG TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 
        4.27        22.26        23.90         8.55        12.59        14.40 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX 
       29.10        27.35        13.84        34.98        59.01         9.07 
TCGA-FI-A2F8 TCGA-KJ-A3U4 TCGA-PG-A7D5 
       25.02         2.43        23.97 

$`DEL PEAK 46(19Q13.43) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OH TCGA-A5-A1OJ 
       42.35        15.95         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O 
        8.02        46.32         5.33         5.16        14.96         1.97 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79         0.85         2.40         3.02         0.49 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       22.26         1.28        36.99        20.65        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67         5.95        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
        8.22        36.89         7.86        12.20        20.91       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        28.54        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        13.28        19.20        16.96        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        33.53        61.18        68.71        33.40        40.50 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        27.32        31.13        38.70 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G8 
        0.23         0.10         0.33         0.13        20.52         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        8.35        14.47         0.13        80.38        56.91        46.75 
TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       43.13        48.76        40.67        44.71        32.55        28.64 
TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 
       28.34        30.51        25.91        23.01        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.10        17.85        11.01         4.11         8.71       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        15.29        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        33.11         5.03        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        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
        7.92        38.37        36.49        28.27        10.72        41.52 
TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       48.56        23.47        43.30        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        9.57        35.67        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-A26L 
       34.98         6.21        10.16        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        23.47 
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        67.20        88.34        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        62.79 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZO 
       63.58        49.55        63.16        66.48        16.83        19.79 
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-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
       22.55         1.74         4.44        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-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 
        1.41         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         6.77         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-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       44.88         0.26         4.11        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-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       24.33        16.01         7.36        16.80        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1G8 
       12.89        27.16        26.96        16.34         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54         8.15        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       22.78        13.97         6.90        19.27        18.84        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
       19.33         3.62        18.87        22.82        13.45        45.76 
TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       31.04         6.44        17.92         2.14         6.97         3.72 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.29         5.88        40.01        33.99        36.00         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 
       13.84         8.98        96.69        28.93        28.96        26.01 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-PG-A5BC TCGA-PG-A6IB 
       41.06        45.01         1.74        13.15        10.82         9.11 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       12.92         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR 
        4.21         5.52 

  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                         125.42                          191.84 
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                          19.96                           23.11 
[1] "0.0 - 125.4 (20.0)" "0.1 - 191.8 (23.1)"
[1] "hr=" "2.8"
D97V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 46(19Q13.43) MUTATED                                        15
  DEL PEAK 46(19Q13.43) WILD-TYPE                                     365
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 46(19Q13.43) MUTATED                               4
  DEL PEAK 46(19Q13.43) WILD-TYPE                            17
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 46(19Q13.43) MUTATED                                  39
  DEL PEAK 46(19Q13.43) WILD-TYPE                                65
D97V3, multiclass
                                         clus
vv                                        DEL PEAK 46(19Q13.43) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            15
  MIXED SEROUS AND ENDOMETRIOID                                       4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  39
                                         clus
vv                                        DEL PEAK 46(19Q13.43) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             365
  MIXED SEROUS AND ENDOMETRIOID                                        17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V4, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.43) MUTATED    14  44
  DEL PEAK 46(19Q13.43) WILD-TYPE 124 323
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.43) MUTATED     14   44
  DEL PEAK 46(19Q13.43) WILD-TYPE  124  323
     clus
vv    DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE
  NO                             14                             124
  YES                            44                             323
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(19Q13.43) MUTATED    34   6   3   5
  DEL PEAK 46(19Q13.43) WILD-TYPE 317  16  14  25
D97V5, multiclass
    clus
vv   DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE
  R0                            34                             317
  R1                             6                              16
  R2                             3                              14
  RX                             5                              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"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(19Q13.43) MUTATED                                  0     0
  DEL PEAK 46(19Q13.43) WILD-TYPE                                4    19
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(19Q13.43) MUTATED                          14
  DEL PEAK 46(19Q13.43) WILD-TYPE                        76
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 46(19Q13.43) MUTATED                                           1
  DEL PEAK 46(19Q13.43) WILD-TYPE                                         8
                                 vv
clus                              WHITE
  DEL PEAK 46(19Q13.43) MUTATED      41
  DEL PEAK 46(19Q13.43) WILD-TYPE   316
D97V6, multiclass
                                           clus
vv                                          DEL PEAK 46(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 0
  BLACK OR AFRICAN AMERICAN                                            14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                41
                                           clus
vv                                          DEL PEAK 46(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  19
  BLACK OR AFRICAN AMERICAN                                              76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               8
  WHITE                                                                 316
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D97V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.43) MUTATED     3  36
  DEL PEAK 46(19Q13.43) WILD-TYPE  10 314
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.43) MUTATED      3   36
  DEL PEAK 46(19Q13.43) WILD-TYPE   10  314
                        clus
vv                       DEL PEAK 46(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            36
                        clus
vv                       DEL PEAK 46(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             314
[1] 2 2
[1] FALSE

Clustering(98) Variable = DEL PEAK 47(20P12.1) MUTATION ANALYSIS
D98V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(20P12.1) MUTATED    19  12
  DEL PEAK 47(20P12.1) WILD-TYPE 424  48
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            31                            472 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            12                             48 
$`DEL PEAK 47(20P12.1) MUTATED`
TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AP-A05H 
      149.56        60.53        19.96         1.18         0.49        45.53 
TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A3G1 
       36.36        18.25        76.83         4.77        33.53        20.52 
TCGA-AX-A3G4 TCGA-B5-A0K8 TCGA-B5-A1MS TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0MG 
        0.13        17.85       102.31        34.95         7.92        48.56 
TCGA-BG-A0MO TCGA-BG-A18C TCGA-BK-A4ZD TCGA-D1-A161 TCGA-D1-A17M TCGA-DI-A1NO 
       43.04        15.45        16.64        29.33        10.22         9.37 
TCGA-DI-A2QT TCGA-EY-A1GW TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2D2 
       12.39         8.55        29.10         6.44        17.92        36.00 
TCGA-FI-A3PV 
       41.06 

$`DEL PEAK 47(20P12.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
        1.08       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
        3.22       105.37        87.32        74.10        57.53        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV 
       60.53        46.55        38.37        36.82        28.27        20.81 
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-A1OH TCGA-A5-A1OJ 
       42.35        15.95         7.92        11.44        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        8.02        91.04        46.32        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33        14.96         1.08         1.97         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        0.85         2.40         3.02         1.12         0.76         2.24 
TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        1.68         1.64        14.66        22.49        22.26         1.28 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
        0.92        36.99        20.65         1.35        15.62         0.76 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DW 
        1.94        15.95         1.87        16.87         1.71         2.33 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
        0.99         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J 
       23.31        86.07         8.22        39.42        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
        7.86        12.20        20.91        48.79       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LL 
      110.37         3.39        63.16        97.71        31.73        83.97 
TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       27.12        82.52        33.40        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM TCGA-AP-A1DO 
       49.22        25.08        71.67        60.36        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        41.95        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        33.73         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       66.58        34.98        53.92        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 
       40.11        65.88        13.28        19.20        16.96        13.55 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       15.25        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08        30.12        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        68.71        33.40        40.50        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        27.32         2.96        31.13        38.70         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 
        0.10         0.33         0.13         0.20         0.03         0.23 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18         8.35        14.47         0.13        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       46.75        43.13        48.76        40.67        44.71        32.55 
TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K4 
       28.64        28.34        30.51        25.91        23.01        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        11.01         4.11         8.71       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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U 
       40.50        36.82        32.09        33.50        27.35        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       191.84 
TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       50.89        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD 
       12.79       116.25        96.30        78.81        62.14        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       20.94        35.21        34.98        38.37        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MQ TCGA-BG-A0MS 
       10.72        41.52        23.47        43.30        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0VW 
       21.17        20.28        15.42        24.39        26.66        16.34 
TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A0YV 
       34.29        52.64        52.83        56.58        14.83        12.56 
TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 
       13.78        14.73        14.01        15.45        14.27         1.81 
TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        35.67        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         6.21        10.22        10.16        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 
       23.47        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        67.20        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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         1.41         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         6.77         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-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ 
        8.48        44.88         0.26         4.27         4.11        27.16 
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 
       91.96        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       24.33        16.01         7.36        16.80        10.92        18.81 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        31.96        35.05        33.01        27.12        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       24.79        32.38        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       12.89        27.16        26.96        22.26        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO 
       23.34        23.90        22.78        13.97         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       15.81         6.48        19.33        12.59         3.62        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        13.45        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       13.84         2.14         6.97         3.72         5.29         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        34.98        33.99         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       96.69        59.01         9.07        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       26.01        45.01         1.74        13.15         2.43        10.82 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
        9.11        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       18.84        39.95         4.21         5.52 

  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                        149.56                         191.84 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                        19.960                         22.965 
[1] "0.1 - 149.6 (20.0)" "0.0 - 191.8 (23.0)"
[1] "hr=" "3.6"
D98V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 47(20P12.1) MUTATED                                        14
  DEL PEAK 47(20P12.1) WILD-TYPE                                     366
                                vv
clus                             MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 47(20P12.1) MUTATED                               2
  DEL PEAK 47(20P12.1) WILD-TYPE                            19
                                vv
clus                             SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 47(20P12.1) MUTATED                                  15
  DEL PEAK 47(20P12.1) WILD-TYPE                                89
D98V3, multiclass
                                         clus
vv                                        DEL PEAK 47(20P12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           14
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 15
                                         clus
vv                                        DEL PEAK 47(20P12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            366
  MIXED SEROUS AND ENDOMETRIOID                                       19
  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"
D98V4, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     9  22
  DEL PEAK 47(20P12.1) WILD-TYPE 129 345
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      9   22
  DEL PEAK 47(20P12.1) WILD-TYPE  129  345
     clus
vv    DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  NO                             9                            129
  YES                           22                            345
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(20P12.1) MUTATED    18   1   2   5
  DEL PEAK 47(20P12.1) WILD-TYPE 333  21  15  25
D98V5, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  R0                           18                            333
  R1                            1                             21
  R2                            2                             15
  RX                            5                             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"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 47(20P12.1) MUTATED                                  1     1
  DEL PEAK 47(20P12.1) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(20P12.1) MUTATED                           7
  DEL PEAK 47(20P12.1) WILD-TYPE                        83
                                vv
clus                             NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 47(20P12.1) MUTATED                                           1
  DEL PEAK 47(20P12.1) WILD-TYPE                                         8
                                vv
clus                             WHITE
  DEL PEAK 47(20P12.1) MUTATED      20
  DEL PEAK 47(20P12.1) WILD-TYPE   337
D98V6, multiclass
                                           clus
vv                                          DEL PEAK 47(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                            7
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               20
                                           clus
vv                                          DEL PEAK 47(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                337
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     2  24
  DEL PEAK 47(20P12.1) WILD-TYPE  11 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      2   24
  DEL PEAK 47(20P12.1) WILD-TYPE   11  326
                        clus
vv                       DEL PEAK 47(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       DEL PEAK 47(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            326
[1] 2 2
[1] FALSE

Clustering(99) Variable = DEL PEAK 48(22Q13.32) MUTATION ANALYSIS
D99V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 48(22Q13.32) MUTATED   106  22
  DEL PEAK 48(22Q13.32) WILD-TYPE 337  38
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            128                             375 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                             22                              38 
$`DEL PEAK 48(22Q13.32) MUTATED`
TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OH 
       65.75        60.53        36.82        19.96        17.59        36.33 
TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       91.04         7.33        14.96         1.18         1.08         0.39 
TCGA-AJ-A2QL TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       19.79         0.49         1.12         2.24         1.64        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A053 
        1.28         0.92         0.76         1.71        21.99         5.95 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LI 
       39.42        57.80        45.53        48.79         3.39        97.71 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
       41.95        33.73        53.92        28.54        37.78        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       13.55        20.28        36.39         4.77        30.12        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW 
       61.18        33.40        19.36         2.96        38.70         0.33 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-B5-A0K8 
        0.13        20.52         0.03         0.13         0.23        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY 
        4.11        75.72        36.82       102.31        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A0MT 
       12.79       116.25        33.11        34.13        36.49        21.17 
TCGA-BG-A0VZ TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A2AD TCGA-BG-A3PP TCGA-BK-A0CA 
       52.64        12.56        15.45        35.67         6.81        34.98 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ 
       10.22        10.16        67.20        29.95         8.55        22.55 
TCGA-D1-A15X TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 
       29.88        11.51        31.07        18.67         1.41         6.77 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DG TCGA-DI-A1NN 
       28.08        13.22         0.72        18.25         4.27        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EO-A1Y7 
        9.37        12.39        31.10         6.67        24.33        18.81 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ 
       32.38        27.16        22.26        16.34         4.54        23.90 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 
       18.84        17.62         8.55        12.59         3.62        14.40 
TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       45.76        29.10        27.35        13.84         6.44        17.92 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F9 
        5.88        34.98        36.00        96.69         9.07        26.01 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC TCGA-PG-A7D5 
       45.01         1.74        13.15         2.43        10.82        23.97 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`DEL PEAK 48(22Q13.32) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW 
       60.53        46.55        38.37        28.27        20.81        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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92        11.44         9.60         8.02        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        5.33         5.16         1.97         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE 
        0.76         1.68        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-A3QS 
        1.35        15.62         1.94        15.95         1.87        16.87 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
        2.33         0.99         2.70         0.13        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        36.89         7.86        12.20        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        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        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        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        18.25         0.56        13.58        19.82 
TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       29.69        68.35        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       66.58        34.98        12.26        51.09        27.39        30.02 
TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       60.66        35.01        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       19.20        15.25        12.43        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2HA 
       54.12        67.50        25.12        11.08        33.53        68.71 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       40.50        26.33        17.75        27.32        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.10         0.20         1.18         8.35        14.47         0.13 
TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       80.38        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 
       44.71        32.55        28.64        28.34        30.51        25.91 
TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11E 
       23.01        17.88        13.74        17.10        11.01         8.71 
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        45.90        43.96 
TCGA-B5-A11O TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        32.09        33.50        27.35        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       191.84        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        11.70        15.29        96.30        78.81        62.14 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
        5.03        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98         7.92        38.37        28.27 
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-A0MS TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV 
       39.32        30.81        20.28        15.42        24.39        26.66 
TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 
       16.34        34.29        52.83        56.58        14.83        13.78 
TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 
       14.73        14.01        15.45        14.27         1.81         9.57 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A13B 
       23.70        20.12        11.31        35.90         6.21        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        23.47        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        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A101 
       19.79         0.56         4.87        28.67        23.93         1.74 
TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15Z TCGA-D1-A160 
        4.44        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         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KZ 
       41.42         8.48        44.88         0.26         4.11        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QY TCGA-E6-A1LX 
       16.31        39.29        36.62        24.30        91.96        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36        17.06         2.37        16.01         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        31.96        35.05        33.01        27.12 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        24.79        19.40        34.39        19.36        35.15 
TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       12.89        26.96         6.21        14.99         8.15        24.36 
TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.34        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        17.88        15.09        16.11        12.43        15.81 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP 
        6.48        19.33        18.87        22.82        13.45        31.04 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
        2.14         6.97         3.72         5.29        40.01        33.99 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 
        7.99        13.84         8.98        59.01        28.93        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       25.02        41.06         9.11        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       39.95         4.21         5.52 

  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                         116.25                          191.84 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                          18.74                           24.13 
[1] "0.0 - 116.2 (18.7)" "0.1 - 191.8 (24.1)"
[1] "hr=" "2.1"
D99V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                                        51
  DEL PEAK 48(22Q13.32) WILD-TYPE                                     329
                                 vv
clus                              MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 48(22Q13.32) MUTATED                              10
  DEL PEAK 48(22Q13.32) WILD-TYPE                            11
                                 vv
clus                              SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                                  68
  DEL PEAK 48(22Q13.32) WILD-TYPE                                36
D99V3, multiclass
                                         clus
vv                                        DEL PEAK 48(22Q13.32) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            51
  MIXED SEROUS AND ENDOMETRIOID                                      10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  68
                                         clus
vv                                        DEL PEAK 48(22Q13.32) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             329
  MIXED SEROUS AND ENDOMETRIOID                                        11
  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"
D99V4, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED    25 104
  DEL PEAK 48(22Q13.32) WILD-TYPE 113 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED     25  104
  DEL PEAK 48(22Q13.32) WILD-TYPE  113  263
     clus
vv    DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  NO                             25                             113
  YES                           104                             263
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(22Q13.32) MUTATED    84   6   6  11
  DEL PEAK 48(22Q13.32) WILD-TYPE 267  16  11  19
D99V5, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  R0                            84                             267
  R1                             6                              16
  R2                             6                              11
  RX                            11                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 48(22Q13.32) MUTATED                                  1     1
  DEL PEAK 48(22Q13.32) WILD-TYPE                                3    18
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(22Q13.32) MUTATED                          34
  DEL PEAK 48(22Q13.32) WILD-TYPE                        56
                                 vv
clus                              NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER
  DEL PEAK 48(22Q13.32) MUTATED                                           2
  DEL PEAK 48(22Q13.32) WILD-TYPE                                         7
                                 vv
clus                              WHITE
  DEL PEAK 48(22Q13.32) MUTATED      85
  DEL PEAK 48(22Q13.32) WILD-TYPE   272
D99V6, multiclass
                                           clus
vv                                          DEL PEAK 48(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                            34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                                85
                                           clus
vv                                          DEL PEAK 48(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  18
  BLACK OR AFRICAN AMERICAN                                              56
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               7
  WHITE                                                                 272
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED     6  92
  DEL PEAK 48(22Q13.32) WILD-TYPE   7 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED      6   92
  DEL PEAK 48(22Q13.32) WILD-TYPE    7  258
                        clus
vv                       DEL PEAK 48(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            92
                        clus
vv                       DEL PEAK 48(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             258
[1] 2 2
[1] FALSE

Clustering(100) Variable = DEL PEAK 49(XP21.1) MUTATION ANALYSIS
D100V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 49(XP21.1) MUTATED    59  18
  DEL PEAK 49(XP21.1) WILD-TYPE 384  42
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           77                           426 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           18                            42 
$`DEL PEAK 49(XP21.1) MUTATED`
TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP 
       60.53        36.82        17.59        36.33        91.04        14.96 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3I9 TCGA-AJ-A3QS TCGA-AJ-A3TW 
        1.08         0.49         1.12         1.28        16.87         1.71 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI 
        5.95        57.80        45.53        36.89        48.79        97.71 
TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 
        0.56        53.92        16.96        67.50        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0JN 
       30.12        61.18        19.36         0.03         0.13        80.38 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY 
       23.01        17.85       113.36        36.82        50.89        11.87 
TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV 
       12.79        33.11        34.95         7.92        36.49        12.56 
TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16V 
       15.45        10.22        16.64        11.51        31.07         1.41 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-DI-A1NO TCGA-DI-A2QT 
       28.08        13.22         2.07         4.27         9.37        12.39 
TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ 
       91.96        24.33        10.92        32.38        19.40        27.16 
TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OQ 
       22.26        23.90        18.84         8.55        13.45        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EU 
       27.35         6.44        17.92         3.72        36.00        96.69 
TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A5BC 
       28.93        41.06        13.15         2.43        10.82 

$`DEL PEAK 49(XP21.1) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
        1.08       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-A0GI 
       32.78         3.22       105.37        87.32        74.10        57.53 
TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       65.75        60.53        46.55        38.37        28.27        20.81 
TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA 
       23.21        68.65        19.96        19.59        24.62        29.06 
TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        11.44         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M 
       46.32        28.64         5.33         5.16         7.33         1.18 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
        1.97         0.39        19.79         0.85         2.40         3.02 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76         2.24         1.68         1.64        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26         0.92        36.99        20.65         1.35        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DW TCGA-AJ-A6NU 
        0.76         1.94        15.95         1.87         2.33         0.99 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
        2.70         0.13        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
        8.22        39.42         7.86        12.20        20.91       125.42 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
      117.99       110.37         3.39        63.16        36.36        31.73 
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-A0LS TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DM 
       63.06        49.22        25.08        71.67        60.36        55.89 
TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        41.95        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        18.25        33.73        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       19.82        29.69        68.35        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H 
       45.99        66.58        34.98        12.26        51.09        27.39 
TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ 
       30.02        60.66        35.01        28.54        37.78        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        13.55        15.25 
TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       20.28        12.43        20.05        76.83        72.56        54.12 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12        36.39        71.24        33.53        68.71        33.40 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       40.50        26.33        17.75        27.32         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       38.70         0.23         0.10         0.33         0.13         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
       20.52         0.23         1.18         8.35        14.47         0.13 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        46.75        43.13        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       13.74        17.10        11.01         4.11         8.71       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        45.90        43.96        40.50 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       32.09        33.50        27.35        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       191.84       102.31        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.70        11.70        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14         5.03        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        34.98        38.37        28.27 
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-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT 
       39.32        30.81        21.17        20.28        15.42        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 
       26.66        16.34        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-A220 
       14.83        13.78        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
        1.81         9.57        35.67        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
        6.81        35.90        34.98         6.21        10.16        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 
       23.47        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        67.20        88.34 
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 
       62.79        63.58        49.55        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       19.79        29.95         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A102 TCGA-D1-A103 TCGA-D1-A15V 
       23.93        22.55         1.74         4.44        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-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
       18.67         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         6.77         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       18.25        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH 
        3.52        41.42         8.48        44.88         0.26         4.11 
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        48.36        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.01         7.36        16.80        18.81        37.71        31.96 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       35.05        33.01        27.12        57.60        24.79        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1G7 
       19.36        35.15        12.89        26.96        16.34         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54         8.15        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       23.34        22.78        13.97         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX 
       17.62        15.09        16.11        12.43        15.81         6.48 
TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       19.33        12.59         3.62        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       45.76        31.04        13.84         2.14         6.97         5.29 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        34.98        33.99         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        59.01         9.07        28.96        25.02        26.01 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       45.01         1.74         9.11        23.97        12.92         7.00 
TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
       11.24         6.97        18.84        39.95         4.21         5.52 

  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                       113.36                        191.84 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                        17.92                         23.34 
[1] "0.0 - 113.4 (17.9)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.6"
D100V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 49(XP21.1) MUTATED                                        28
  DEL PEAK 49(XP21.1) WILD-TYPE                                     352
                               vv
clus                            MIXED SEROUS AND ENDOMETRIOID
  DEL PEAK 49(XP21.1) MUTATED                               3
  DEL PEAK 49(XP21.1) WILD-TYPE                            18
                               vv
clus                            SEROUS ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 49(XP21.1) MUTATED                                  46
  DEL PEAK 49(XP21.1) WILD-TYPE                                58
D100V3, multiclass
                                         clus
vv                                        DEL PEAK 49(XP21.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          28
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                46
                                         clus
vv                                        DEL PEAK 49(XP21.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           352
  MIXED SEROUS AND ENDOMETRIOID                                      18
  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"
D100V4, binary
                               cls
clus                              0   1
  DEL PEAK 49(XP21.1) MUTATED    17  60
  DEL PEAK 49(XP21.1) WILD-TYPE 121 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED     17   60
  DEL PEAK 49(XP21.1) WILD-TYPE  121  307
     clus
vv    DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  NO                           17                           121
  YES                          60                           307
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 49(XP21.1) MUTATED    50   2   6   5
  DEL PEAK 49(XP21.1) WILD-TYPE 301  20  11  25
D100V5, multiclass
    clus
vv   DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  R0                          50                           301
  R1                           2                            20
  R2                           6                            11
  RX                           5                            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"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 49(XP21.1) MUTATED                                  1     1
  DEL PEAK 49(XP21.1) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 49(XP21.1) MUTATED                          25
  DEL PEAK 49(XP21.1) WILD-TYPE                        65
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 49(XP21.1) MUTATED                                           1    44
  DEL PEAK 49(XP21.1) WILD-TYPE                                         8   313
D100V6, multiclass
                                           clus
vv                                          DEL PEAK 49(XP21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              44
                                           clus
vv                                          DEL PEAK 49(XP21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               313
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D100V7, binary
                               cls
clus                              0   1
  DEL PEAK 49(XP21.1) MUTATED     4  51
  DEL PEAK 49(XP21.1) WILD-TYPE   9 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED      4   51
  DEL PEAK 49(XP21.1) WILD-TYPE    9  299
                        clus
vv                       DEL PEAK 49(XP21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       DEL PEAK 49(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           299
[1] 2 2
[1] FALSE
