[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/15094079/UCEC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/15106279/transformed.cor.cli.txt"

nPatients in clinical file=537, in cluster file=539, common to both=528
[1] 100 528
[1] "AMP PEAK  1(1P35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           55                           473 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           55                           473 
[1] "AMP PEAK  2(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           72                           456 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           72                           456 
[1] "AMP PEAK  3(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           95                           433 
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           95                           433 
[1] "AMP PEAK  4(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                          236                           292 
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                          236                           292 
[1] "AMP PEAK  5(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                        249                         279 
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                        249                         279 
[1] "AMP PEAK  6(1Q44) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                        213                         315 
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                        213                         315 
[1] "AMP PEAK  7(2P24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                          118                           410 
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                          118                           410 
[1] "AMP PEAK  8(2Q13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                        116                         412 
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                        116                         412 
[1] "AMP PEAK  9(3P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           80                           448 
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           80                           448 
[1] "AMP PEAK 10(3P14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           63                           465 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           63                           465 
[1] "AMP PEAK 11(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          171                           357 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          171                           357 
[1] "AMP PEAK 12(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                          159                           369 
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                          159                           369 
[1] "AMP PEAK 13(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           52                           476 
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           52                           476 
[1] "AMP PEAK 14(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            88                            440 
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            88                            440 
[1] "AMP PEAK 15(5Q35.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           53                           475 
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           53                           475 
[1] "AMP PEAK 16(6P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                          114                           414 
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                          114                           414 
[1] "AMP PEAK 17(6P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                          104                           424 
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                          104                           424 
[1] "AMP PEAK 18(6Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           84                           444 
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           84                           444 
[1] "AMP PEAK 19(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           90                           438 
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           90                           438 
[1] "AMP PEAK 20(8P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                           125                            403 
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                           125                            403 
[1] "AMP PEAK 21(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                           161                            367 
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                           161                            367 
[1] "AMP PEAK 22(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                           206                            322 
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                           206                            322 
[1] "AMP PEAK 23(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                           212                            316 
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                           212                            316 
[1] "AMP PEAK 24(9P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           64                           464 
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           64                           464 
[1] "AMP PEAK 25(9Q34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                           38                           490 
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                           38                           490 
[1] "AMP PEAK 26(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                           143                            385 
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                           143                            385 
[1] "AMP PEAK 27(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            50                            478 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            50                            478 
[1] "AMP PEAK 28(11Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            70                            458 
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            70                            458 
[1] "AMP PEAK 29(11Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            56                            472 
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            56                            472 
[1] "AMP PEAK 30(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            92                            436 
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            92                            436 
[1] "AMP PEAK 31(12Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             84                             444 
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             84                             444 
[1] "AMP PEAK 32(12Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            97                            431 
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            97                            431 
[1] "AMP PEAK 33(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                          57                          471 
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                          57                          471 
[1] "AMP PEAK 34(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            63                            465 
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            63                            465 
[1] "AMP PEAK 35(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             76                             452 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             76                             452 
[1] "AMP PEAK 36(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            37                            491 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            37                            491 
[1] "AMP PEAK 37(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            64                            464 
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            64                            464 
[1] "AMP PEAK 38(17Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            71                            457 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            71                            457 
[1] "AMP PEAK 39(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          74                          454 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          74                          454 
[1] "AMP PEAK 40(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                           102                            426 
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                           102                            426 
[1] "AMP PEAK 41(18P11.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             94                             434 
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             94                             434 
[1] "AMP PEAK 42(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            68                            460 
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            68                            460 
[1] "AMP PEAK 43(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            97                            431 
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            97                            431 
[1] "AMP PEAK 44(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                         116                          412 
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                         116                          412 
[1] "AMP PEAK 45(20P13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                         116                          412 
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                         116                          412 
[1] "AMP PEAK 46(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                            149                             379 
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                            149                             379 
[1] "AMP PEAK 47(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                            149                             379 
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                            149                             379 
[1] "AMP PEAK 48(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                            150                             378 
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                            150                             378 
[1] "AMP PEAK 49(22Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            62                            466 
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            62                            466 
[1] "AMP PEAK 50(XP11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            89                            439 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            89                            439 
[1] "AMP PEAK 51(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         89                         439 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         89                         439 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            69                            459 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            69                            459 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            79                            449 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            79                            449 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           26                           502 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           26                           502 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           46                           482 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           46                           482 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           52                           476 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           52                           476 
[1] "DEL PEAK  6(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           77                           451 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           77                           451 
[1] "DEL PEAK  7(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            42                            486 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            42                            486 
[1] "DEL PEAK  8(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           89                           439 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           89                           439 
[1] "DEL PEAK  9(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           93                           435 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           93                           435 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          102                           426 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          102                           426 
[1] "DEL PEAK 11(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          127                           401 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          127                           401 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          109                           419 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          109                           419 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         45                         483 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         45                         483 
[1] "DEL PEAK 14(7P22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           70                           458 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           70                           458 
[1] "DEL PEAK 15(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            39                            489 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            39                            489 
[1] "DEL PEAK 16(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           53                           475 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           53                           475 
[1] "DEL PEAK 17(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           62                           466 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           62                           466 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          115                           413 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          115                           413 
[1] "DEL PEAK 19(8P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          113                           415 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          113                           415 
[1] "DEL PEAK 20(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         76                         452 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         76                         452 
[1] "DEL PEAK 21(9Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          126                           402 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          126                           402 
[1] "DEL PEAK 22(9Q34.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          128                           400 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          128                           400 
[1] "DEL PEAK 23(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             75                             453 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             75                             453 
[1] "DEL PEAK 24(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                           102                            426 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                           102                            426 
[1] "DEL PEAK 25(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            70                            458 
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            70                            458 
[1] "DEL PEAK 26(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          92                          436 
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          92                          436 
[1] "DEL PEAK 27(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            53                            475 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            53                            475 
[1] "DEL PEAK 28(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             63                             465 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             63                             465 
[1] "DEL PEAK 29(13Q11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          94                          434 
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          94                          434 
[1] "DEL PEAK 30(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           103                            425 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           103                            425 
[1] "DEL PEAK 31(14Q13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            71                            457 
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            71                            457 
[1] "DEL PEAK 32(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           136                            392 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           136                            392 
[1] "DEL PEAK 33(15Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                         113                          415 
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                         113                          415 
[1] "DEL PEAK 34(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            90                            438 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            90                            438 
[1] "DEL PEAK 35(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                         150                          378 
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                         150                          378 
[1] "DEL PEAK 36(16Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                           154                            374 
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                           154                            374 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           162                            366 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           162                            366 
[1] "DEL PEAK 38(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                           119                            409 
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                           119                            409 
[1] "DEL PEAK 39(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                           124                            404 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                           124                            404 
[1] "DEL PEAK 40(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                           101                            427 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                           101                            427 
[1] "DEL PEAK 41(17Q21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                            109                             419 
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                            109                             419 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            89                            439 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            89                            439 
[1] "DEL PEAK 43(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          95                          433 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          95                          433 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           151                            377 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           151                            377 
[1] "DEL PEAK 45(19P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          57                          471 
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          57                          471 
[1] "DEL PEAK 46(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             65                             463 
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             65                             463 
[1] "DEL PEAK 47(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            35                            493 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            35                            493 
[1] "DEL PEAK 48(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            136                             392 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            136                             392 
[1] "DEL PEAK 49(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           84                           444 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           84                           444 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCH_NUMBER"                          

Input Data has 20 rows and 528 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=67,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=422,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE excluded in the analysis because there is no case of (both >= 3) in the table below"
              ENDOMETRIAL OTHER  SPECIFY
freq.values   "527"       "1"           
freq.contrast "1"         "527"         
both >= 3     "FALSE"     "FALSE"       
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=35,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 528 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"                        
[2] "HISTOLOGICAL_TYPE"                     
[3] "RADIATIONS_RADIATION_REGIMENINDICATION"
[4] "COMPLETENESS_OF_RESECTION"             
[5] "RACE"                                  
[6] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=59, 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    44  11
  AMP PEAK  1(1P35.2) WILD-TYPE 413  58
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           55                           471 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                           11                            58 
$`AMP PEAK  1(1P35.2) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K2 
       41.06        37.02        65.75        19.96        11.44        91.04 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
        1.12        18.90         1.64        63.91        57.80        45.53 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1CF 
       48.79        97.71        21.90        36.13        37.78        76.83 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       71.24        19.36        20.52         0.30         0.26         0.30 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A1MS TCGA-B5-A3S1 TCGA-BG-A18C 
       80.38        27.29        17.85       102.31        29.65        15.45 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 
       16.64        67.20        22.55        11.51        31.07        14.73 
TCGA-D1-A17K TCGA-D1-A1NX TCGA-D1-A3JP TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A3KU 
       28.08        18.25        16.93        49.15        37.71        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A3L3 TCGA-FI-A2CY TCGA-FI-A2D2 
       16.34        23.90        11.08        27.35        41.06        39.95 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-PG-A5BC 
       96.69        59.01        29.23        23.74         9.47        23.24 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK  1(1P35.2) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         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-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK 
       29.39         2.40        34.36        34.16         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC 
       14.66        22.49        22.26        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.65        21.21        15.62        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        36.89        23.87        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-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        46.78        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-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-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-A2HG 
       40.80        61.18        81.37        34.32        46.49        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G8 
        0.20         0.56        43.82         0.20         1.38         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        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-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-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        33.11        14.27        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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        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-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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        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-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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       27.42        29.92        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-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-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       36.62        24.30        35.38         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        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-A22R 
       27.32        16.04         7.36        16.80        10.92        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        26.96        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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        10.19        14.40        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR 
       20.05        45.76        31.04        29.10        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX 
       40.01        39.88         7.99        13.84         8.98         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-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
        7.76        14.04         2.43        13.28        26.10        18.21 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.07        18.28         0.23 

  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                       102.31                        191.84 
  AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE 
                        27.29                         23.21 
[1] "0.1 - 102.3 (27.3)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.5"
D1V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  1(1P35.2) MUTATED                                        16
  AMP PEAK  1(1P35.2) WILD-TYPE                                     379
                               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                                  34
  AMP PEAK  1(1P35.2) WILD-TYPE                                78
D1V3, multiclass
                                         clus
vv                                        AMP PEAK  1(1P35.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          16
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                34
                                         clus
vv                                        AMP PEAK  1(1P35.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           379
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D1V4, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P35.2) MUTATED    16  39
  AMP PEAK  1(1P35.2) WILD-TYPE 125 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P35.2) MUTATED     16   39
  AMP PEAK  1(1P35.2) WILD-TYPE  125  348
     clus
vv    AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE
  NO                           16                           125
  YES                          39                           348
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P35.2) MUTATED    35   2   2   7
  AMP PEAK  1(1P35.2) WILD-TYPE 328  21  15  28
D1V5, multiclass
    clus
vv   AMP PEAK  1(1P35.2) MUTATED AMP PEAK  1(1P35.2) WILD-TYPE
  R0                          35                           328
  R1                           2                            21
  R2                           2                            15
  RX                           7                            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  1(1P35.2) MUTATED                                  0     1
  AMP PEAK  1(1P35.2) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  1(1P35.2) MUTATED                          15
  AMP PEAK  1(1P35.2) WILD-TYPE                        86
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  1(1P35.2) MUTATED                                           2    30
  AMP PEAK  1(1P35.2) WILD-TYPE                                         7   336
D1V6, multiclass
                                           clus
vv                                          AMP PEAK  1(1P35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              30
                                           clus
vv                                          AMP PEAK  1(1P35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            86
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               336
[1] 5 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  35
  AMP PEAK  1(1P35.2) WILD-TYPE  12 332
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P35.2) MUTATED      2   35
  AMP PEAK  1(1P35.2) WILD-TYPE   12  332
                        clus
vv                       AMP PEAK  1(1P35.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          35
                        clus
vv                       AMP PEAK  1(1P35.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           332
[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    55  17
  AMP PEAK  2(1P34.2) WILD-TYPE 402  52
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           72                           454 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                           17                            52 
$`AMP PEAK  2(1P34.2) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A3LP TCGA-AJ-A23M 
       41.06        37.02        65.75        11.44        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
       14.43        34.16        10.19        16.87        20.78        21.99 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B 
       45.53        48.79       125.42        21.90        36.13        53.92 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR 
       28.54        37.78        16.96        76.83        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       30.12        71.24        20.52         1.38         0.30         0.26 
TCGA-B5-A0JN TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C 
       80.38         4.11        75.72        29.65        34.13        15.45 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 
       16.64        67.20        22.55        11.51        31.07        14.73 
TCGA-D1-A2G7 TCGA-DI-A1NO TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A3AS TCGA-EO-A3KU 
       44.88         9.37        49.15        37.71        34.39        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
       16.34        23.90        15.81        11.08        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 
       14.40        20.05        29.10        11.38        41.06        39.95 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-JU-AAVI 
       96.69        59.01         9.07        25.02        29.23         7.76 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-SL-A6J9 
       14.04        13.28         9.47        26.10        18.21         0.07 

$`AMP PEAK  2(1P34.2) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-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-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16         7.33        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36         1.12         0.76        18.90         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        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
       14.76        16.87        22.32        12.82         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        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       57.80        36.89        23.87        12.20        20.91       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        46.78        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-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-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-A2H2 TCGA-AX-A2H7 
       72.56        54.12        67.50        25.12         4.77        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20         0.56        43.82         0.20         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        56.91        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        27.29        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-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-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-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        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        22.06        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-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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        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-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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       27.42        29.92        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-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-A3DA 
        1.05         3.95         3.52        41.42         8.48         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        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       110.10        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        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        19.40        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        26.96        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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-A1GX TCGA-EY-A1H0 
       17.62        15.09        16.11        12.43         6.48        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        45.76        31.04        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EY 
       40.01        39.88         7.99        13.84         8.98        28.93 
TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       28.96        41.06        45.01         1.74         2.43        23.74 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       23.24        15.45        23.97        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                         0.07                          0.13 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       125.42                        191.84 
  AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE 
                       22.125                        23.425 
[1] "0.1 - 125.4 (22.1)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.2"
D2V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  2(1P34.2) MUTATED                                        21
  AMP PEAK  2(1P34.2) WILD-TYPE                                     374
                               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                                  44
  AMP PEAK  2(1P34.2) WILD-TYPE                                68
D2V3, multiclass
                                         clus
vv                                        AMP PEAK  2(1P34.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          21
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                44
                                         clus
vv                                        AMP PEAK  2(1P34.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           374
  MIXED SEROUS AND ENDOMETRIOID                                      14
  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"
D2V4, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED    15  57
  AMP PEAK  2(1P34.2) WILD-TYPE 126 330
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED     15   57
  AMP PEAK  2(1P34.2) WILD-TYPE  126  330
     clus
vv    AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  NO                           15                           126
  YES                          57                           330
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1P34.2) MUTATED    44   4   5   7
  AMP PEAK  2(1P34.2) WILD-TYPE 319  19  12  28
D2V5, multiclass
    clus
vv   AMP PEAK  2(1P34.2) MUTATED AMP PEAK  2(1P34.2) WILD-TYPE
  R0                          44                           319
  R1                           4                            19
  R2                           5                            12
  RX                           7                            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  2(1P34.2) MUTATED                                  0     1
  AMP PEAK  2(1P34.2) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  2(1P34.2) MUTATED                          22
  AMP PEAK  2(1P34.2) WILD-TYPE                        79
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  2(1P34.2) MUTATED                                           2    39
  AMP PEAK  2(1P34.2) WILD-TYPE                                         7   327
D2V6, multiclass
                                           clus
vv                                          AMP PEAK  2(1P34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              39
                                           clus
vv                                          AMP PEAK  2(1P34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            79
  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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1P34.2) MUTATED     2  47
  AMP PEAK  2(1P34.2) WILD-TYPE  12 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1P34.2) MUTATED      2   47
  AMP PEAK  2(1P34.2) WILD-TYPE   12  320
                        clus
vv                       AMP PEAK  2(1P34.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       AMP PEAK  2(1P34.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           320
[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    80  15
  AMP PEAK  3(1P22.3) WILD-TYPE 377  54
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           95                           431 
  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                           15                            54 
$`AMP PEAK  3(1P22.3) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GN TCGA-A5-A1OG TCGA-A5-A3LP 
       36.69        37.02        83.51        60.53        11.44        14.96 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NH 
        1.18        10.26        29.39        34.16         1.64        10.19 
TCGA-AJ-A6NU TCGA-AP-A051 TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LE 
       20.78        83.67        45.53        48.79       125.42       110.37 
TCGA-AP-A0LF TCGA-AP-A0LL TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 
        3.39        83.97        31.30        35.54        10.42        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A060 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW 
       21.90        36.13        35.34        34.98        35.01        37.78 
TCGA-AX-A0J1 TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A3FS 
       65.88        11.08         4.77        61.18        81.37         0.23 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0K7 
       20.52         1.38         0.30        80.38        56.91        17.10 
TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11Q TCGA-B5-A11Z TCGA-B5-A1MS TCGA-B5-A1MZ 
       17.85        75.72        32.09        17.36       102.31        15.29 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A18C 
       29.65        34.13        21.17        15.42        52.83        15.45 
TCGA-BG-A3EW TCGA-BK-A13B TCGA-BK-A4ZD TCGA-BS-A0U7 TCGA-BS-A0U9 TCGA-BS-A0UT 
       11.31        31.76        16.64        30.74        67.20        72.72 
TCGA-D1-A160 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17A TCGA-D1-A2G5 TCGA-D1-A3DA 
        3.68        11.51        18.67         1.58        41.42         0.26 
TCGA-DI-A0WH TCGA-DI-A1NO TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       16.31         9.37        34.39        22.26        16.34         4.54 
TCGA-EY-A1GD TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       53.88        23.90        19.27        17.88        16.11        12.43 
TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A2D2 
       10.19        20.05        45.76        29.10        14.70        39.95 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-KP-A3W1 
       96.69        59.01        28.96        25.02         7.76         9.47 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       26.10        23.97        12.92         7.00         0.07 

$`AMP PEAK  3(1P22.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0GA TCGA-A5-A0GB 
       41.06        10.29       106.88       149.56        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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-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-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        7.33        14.43         0.39        19.79         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76        18.90         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A053 
       22.32        12.82         2.70         0.13        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        63.91        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LG TCGA-AP-A0LH 
       23.87        12.20        20.91       117.99        63.16        36.36 
TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LO TCGA-AP-A0LP 
       97.71        31.73        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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 
       55.89        46.78        49.15         6.71        30.90        27.85 
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-A062 TCGA-AX-A063 TCGA-AX-A06B TCGA-AX-A06D TCGA-AX-A06F 
       46.45        45.99        66.58        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-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-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HC 
       25.12        36.39        30.12        71.24        40.80        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13        64.93         0.20         0.56        43.82         0.20 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-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        27.29        17.88 
TCGA-B5-A0K6 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       13.74        11.01         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-A11P 
       88.34        54.44        45.90        43.96        40.50        36.82 
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-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-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-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        14.27        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        22.06        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-A0MU TCGA-BG-A0VT 
       43.30        43.04        39.32        30.81        20.28        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        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-A3PP 
        1.81         9.57        20.02        23.70        20.12         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13C 
       35.90        34.98         6.21        10.22        10.16        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-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       96.49        97.41        88.34        85.84        82.39        81.57 
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-A161 
       21.99        39.48        30.08        29.88         1.91        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02        14.73         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95         3.52         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT 
       27.16        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       110.10        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        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        51.42        19.40        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        26.96        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        6.21        14.99        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78        13.97         6.90        18.84        17.62        15.09 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
       15.81        11.08         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       18.87        22.82        31.04        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       17.92        14.14        19.89        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX 
       41.06        39.88         7.99        13.84         8.98         9.07 
TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       28.93        29.23        41.06        45.01         1.74        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
        2.43        23.74        13.28        18.21        23.24        15.45 
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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.23 

  AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE 
                         0.07                          0.13 
  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 
                        22.26                         23.34 
[1] "0.1 - 125.4 (22.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  3(1P22.3) MUTATED                                        55
  AMP PEAK  3(1P22.3) WILD-TYPE                                     340
                               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                                  35
  AMP PEAK  3(1P22.3) WILD-TYPE                                77
D3V3, multiclass
                                         clus
vv                                        AMP PEAK  3(1P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          55
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                35
                                         clus
vv                                        AMP PEAK  3(1P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           340
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                               cls
clus                              0   1
  AMP PEAK  3(1P22.3) MUTATED    22  73
  AMP PEAK  3(1P22.3) WILD-TYPE 119 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P22.3) MUTATED     22   73
  AMP PEAK  3(1P22.3) WILD-TYPE  119  314
     clus
vv    AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE
  NO                           22                           119
  YES                          73                           314
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(1P22.3) MUTATED    63   3   2   7
  AMP PEAK  3(1P22.3) WILD-TYPE 300  20  15  28
D3V5, multiclass
    clus
vv   AMP PEAK  3(1P22.3) MUTATED AMP PEAK  3(1P22.3) WILD-TYPE
  R0                          63                           300
  R1                           3                            20
  R2                           2                            15
  RX                           7                            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  3(1P22.3) MUTATED                                  1     2
  AMP PEAK  3(1P22.3) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  3(1P22.3) MUTATED                          24
  AMP PEAK  3(1P22.3) WILD-TYPE                        77
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  3(1P22.3) MUTATED                                           2    61
  AMP PEAK  3(1P22.3) WILD-TYPE                                         7   305
D3V6, multiclass
                                           clus
vv                                          AMP PEAK  3(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              61
                                           clus
vv                                          AMP PEAK  3(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            77
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               305
[1] 5 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  64
  AMP PEAK  3(1P22.3) WILD-TYPE  14 303
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1P22.3) MUTATED      0   64
  AMP PEAK  3(1P22.3) WILD-TYPE   14  303
                        clus
vv                       AMP PEAK  3(1P22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       AMP PEAK  3(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           303
[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   196  39
  AMP PEAK  4(1Q21.3) WILD-TYPE 261  30
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                          235                           291 
  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                           39                            30 
$`AMP PEAK  4(1Q21.3) MUTATED`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU 
       32.78        87.32        57.53        60.53        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A3LP 
       20.81        11.44         9.60         8.02        46.32        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF 
        1.18        14.43        10.26        29.39        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF 
       18.90         1.64        22.26        20.81        36.99        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       15.62        10.19        14.76        16.87        16.87        20.78 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A05A 
        0.13        83.67        21.99         5.95        23.31        63.91 
TCGA-AP-A05H TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       45.53        12.20        20.91        48.79       125.42       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        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       36.13        13.58        68.35        72.03        46.45        35.34 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1C8 
       66.58        34.98        35.01        37.78        65.88        13.55 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR 
       20.28        76.83        72.56        54.12        67.50        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HH 
        4.77        71.24        40.80        61.18        81.37        17.75 
TCGA-AX-A2IN TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 
       31.13        20.52         1.38         0.30         0.26         1.18 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV 
       14.47         0.39        80.38        56.91        43.13        40.67 
TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11I 
       28.34        17.88        13.74        17.10        11.01        75.72 
TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MS 
       36.82        32.09        33.50        27.35        17.36       102.31 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       11.87        15.29        12.79        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.13        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       22.06        43.04        39.32        30.81        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A186 TCGA-BG-A18C 
       15.42        24.39        26.66        52.83        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-A4ZD TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 
       31.76        24.99        16.64        61.87        30.74        67.20 
TCGA-BS-A0UT TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A102 
       72.72        63.16        16.83         8.55         0.56         4.44 
TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 
        3.68         0.66        11.51        18.67         3.95        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17R 
       18.02         1.58         7.00        26.37        10.22        11.15 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
       18.02         2.07        41.42         8.48        44.88         0.26 
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       110.10 
TCGA-E6-A1LZ TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       48.36         6.67        27.32         7.36        10.92        37.71 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       51.52        34.39        27.16        26.96        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF TCGA-EY-A1GK TCGA-EY-A1GO 
        6.21         4.54        53.88        27.16        22.78        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-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON 
       15.81         6.48        12.59        10.19        14.40        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A549 
       45.76        31.04        29.10        27.35        11.38        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       14.70        16.96        39.95        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        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 
        2.43        23.74        13.28         9.47        26.10        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A917 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       12.92         7.00         6.97        14.83         4.44         0.07 
TCGA-SL-A6JA 
        0.23 

$`AMP PEAK  4(1Q21.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0G1 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       41.06       106.88       112.54       105.37        74.10        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       60.53        46.55        38.37        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92        36.33        91.04        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        7.33         0.39        19.79         2.40        34.36         0.76 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3OJ 
        1.68        14.66        22.49        17.06        20.65        15.35 
TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A056 TCGA-AP-A059 
       15.95        22.32        12.82         2.70        86.07         8.22 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM 
       57.80        36.89        23.87        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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       71.67        60.36        46.78        49.15         6.71        30.90 
TCGA-AP-A1E3 TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06B 
       27.85         0.56        19.82        29.69        45.99        53.92 
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-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C9 
       43.82        40.11        13.28        19.20        16.96        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HC 
       12.43        20.05        25.12        36.39        30.12        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IO 
       46.49        19.36        26.33        30.74         2.96        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 
        0.23         0.20         0.56        43.82         0.20         0.30 
TCGA-AX-A3G9 TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       18.35        46.75        48.76        44.71        32.55        28.64 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E 
       30.51        25.91        27.29        17.85         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-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 
       40.50        16.73        19.56        19.50        18.41        16.57 
TCGA-B5-A1MR TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A3F9 
      191.84        50.89        14.40        14.70        11.70       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0LW 
       96.30        78.81        62.14        33.11        34.95        18.61 
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-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       23.47        43.30        16.34        34.29        52.64        56.58 
TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       14.83        12.56        14.73        14.01        15.45        14.27 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB 
       20.02        23.70        20.12         6.81        34.98         6.21 
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-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZO 
       59.51        62.79        63.58        49.55        66.48        19.79 
TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 
       29.95         4.87        28.67        23.93        22.55         1.74 
TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A161 
       21.99        39.48        30.08        29.88         1.91        29.33 
TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
       32.58        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-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A179 
        0.69         3.65        17.49        19.53         6.64        14.73 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17N 
        0.99        30.44         1.28        28.01        28.08         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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        0.72        18.25        16.87        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DI-A1BU 
        3.52         4.27        16.93        89.33        10.92        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        35.38        31.10        23.38        17.06 
TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        2.37        16.04        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       66.90        46.26        57.60        51.42        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       35.15        17.19        17.88        14.53        24.89        14.99 
TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM 
       24.36        23.34        23.34        23.90        13.97         6.90 
TCGA-EY-A1GW TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A3QX TCGA-EY-A547 
       11.08        19.33        18.87        22.82        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       14.14         5.88        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-JU-AAVI TCGA-KP-A3W4 
       13.84         8.98        96.69        29.23         7.76        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       23.24        15.45        11.24        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       23.64        14.07        18.28 

  AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE 
                         0.07                          0.20 
  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 
                        20.81                         24.30 
[1] "0.1 - 149.6 (20.8)" "0.2 - 191.8 (24.3)"
[1] "hr=" "1.8"
D4V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  4(1Q21.3) MUTATED                                       154
  AMP PEAK  4(1Q21.3) WILD-TYPE                                     241
                               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                                  72
  AMP PEAK  4(1Q21.3) WILD-TYPE                                40
D4V3, multiclass
                                         clus
vv                                        AMP PEAK  4(1Q21.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         154
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                72
                                         clus
vv                                        AMP PEAK  4(1Q21.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           241
  MIXED SEROUS AND ENDOMETRIOID                                      11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                               cls
clus                              0   1
  AMP PEAK  4(1Q21.3) MUTATED    57 179
  AMP PEAK  4(1Q21.3) WILD-TYPE  84 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q21.3) MUTATED     57  179
  AMP PEAK  4(1Q21.3) WILD-TYPE   84  208
     clus
vv    AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE
  NO                           57                            84
  YES                         179                           208
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(1Q21.3) MUTATED   163   9  10  15
  AMP PEAK  4(1Q21.3) WILD-TYPE 200  14   7  20
D4V5, multiclass
    clus
vv   AMP PEAK  4(1Q21.3) MUTATED AMP PEAK  4(1Q21.3) WILD-TYPE
  R0                         163                           200
  R1                           9                            14
  R2                          10                             7
  RX                          15                            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  4(1Q21.3) MUTATED                                  2     5
  AMP PEAK  4(1Q21.3) WILD-TYPE                                2    15
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  4(1Q21.3) MUTATED                          59
  AMP PEAK  4(1Q21.3) WILD-TYPE                        42
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  4(1Q21.3) MUTATED                                           2   156
  AMP PEAK  4(1Q21.3) WILD-TYPE                                         7   210
D4V6, multiclass
                                           clus
vv                                          AMP PEAK  4(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                               5
  BLACK OR AFRICAN AMERICAN                                          59
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                             156
                                           clus
vv                                          AMP PEAK  4(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      2
  ASIAN                                                                15
  BLACK OR AFRICAN AMERICAN                                            42
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               210
[1] 5 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     4 169
  AMP PEAK  4(1Q21.3) WILD-TYPE  10 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(1Q21.3) MUTATED      4  169
  AMP PEAK  4(1Q21.3) WILD-TYPE   10  198
                        clus
vv                       AMP PEAK  4(1Q21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         169
                        clus
vv                       AMP PEAK  4(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           198
[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   205  44
  AMP PEAK  5(1Q22) WILD-TYPE 252  25
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                        249                         277 
  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                         44                          25 
$`AMP PEAK  5(1Q22) MUTATED`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU 
       32.78        87.32        57.53        60.53        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
       20.81        11.44        36.33         9.60         8.02        46.32 
TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QM 
       28.64        14.96         1.18        14.43        10.26        29.39 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA 
       34.16         1.12        18.90         1.64        22.26        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS 
       36.99        21.21        15.62        10.19        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       16.87        20.78         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       23.31        63.91        45.53        12.20        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LL 
      117.99       110.37         3.39        36.36        97.71        83.97 
TCGA-AP-A0LO TCGA-AP-A1DM TCGA-AP-A1DO TCGA-AP-A1DP TCGA-AP-A1E1 TCGA-AP-A1E4 
       33.40        55.89        31.30        35.54        10.42        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       21.90        36.13        13.58        68.35        72.03        46.45 
TCGA-AX-A060 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW 
       35.34        66.58        34.98        35.01        28.54        37.78 
TCGA-AX-A0J1 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CF 
       65.88        16.96        13.55        15.25        20.28        76.83 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 
       72.56        54.12        67.50        11.08        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A2IO 
       40.80        81.37        19.36        17.75        31.13        64.93 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 
       43.82        20.52         1.38         0.30         0.26         1.18 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JV 
       14.47         0.39        80.38        56.91        43.13        40.67 
TCGA-B5-A0K0 TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       28.34        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A11Z 
        4.11        36.82        32.09        33.50        27.35        17.36 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FH 
      102.31        50.89        11.87        15.29        12.79        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       29.65        41.06        34.13        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS 
       35.21        34.98        22.06        43.04        39.32        30.81 
TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0W1 
       21.17        20.28        15.42        24.39        26.66        52.83 
TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A3EW 
       12.56        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-A26L 
       35.90        10.22        10.16        31.76        24.99        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UT 
       16.64        61.87        30.74        97.41        67.20        72.72 
TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A102 TCGA-D1-A160 
       63.16        16.83         8.55         0.56         4.44         3.68 
TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A176 
        0.66        11.51        33.63        18.67         3.95        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17K TCGA-D1-A17L 
       18.02        14.73         1.58         7.00        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A2G5 
       10.22        11.15        18.25        18.02         2.07        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KZ TCGA-DI-A0WH 
        8.48         0.26         4.27         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       110.10        48.36         6.67        27.32 
TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AZ 
        7.36        10.92        37.71        51.52        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GF 
       26.96        22.26         6.21         4.54        53.88        27.16 
TCGA-EY-A1GK TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78        19.27        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A212 
       16.11        12.43        15.81         6.48        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       14.40        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A4KR TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2D2 TCGA-FI-A2EW 
       11.38        19.89        14.70        16.96        39.95        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        29.23        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       45.01         1.74        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 TCGA-QS-A744 
        9.47        26.10        23.97        12.92         6.97        14.83 
TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44         0.07         0.23 

$`AMP PEAK  5(1Q22) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0G1 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GJ 
       41.06       106.88       112.54       105.37        74.10        65.75 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       60.53        46.55        38.37        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A2QK 
        7.92        91.04         5.33         5.16         7.33         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       19.79         2.40        34.36         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NE TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV 
       22.49        17.06        20.65        15.35        15.95        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J 
       12.82         2.70        86.07         8.22        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A0L9 TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN 
       23.87       125.42        63.16        31.73        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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E3 
       60.36        46.78        49.15         6.71        30.90        27.85 
TCGA-AW-A1PO TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A062 TCGA-AX-A06B TCGA-AX-A06D 
        0.56        19.82        29.69        45.99        53.92        12.26 
TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IZ TCGA-AX-A0J0 
       51.09        27.39        30.02        60.66        43.82        40.11 
TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CN TCGA-AX-A1CP 
       13.28        19.20        12.43        20.05        25.12        36.39 
TCGA-AX-A2H2 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
        4.77        61.18        34.32        46.49        26.33        30.74 
TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 
        2.96         0.23         0.20         0.56         0.20         0.30 
TCGA-AX-A3G9 TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ 
       18.35        46.75        48.76        44.71        32.55        28.64 
TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       30.51        25.91        17.85         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-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A121 TCGA-B5-A1MR 
       16.73        19.56        19.50        18.41        16.57       191.84 
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-A187 
       16.34        34.29        52.64        56.58        14.83        14.73 
TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 
       14.01        15.45        14.27        20.02        23.70        20.12 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
        6.81        34.98         6.21        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-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       67.99        96.49        88.34        85.84        82.39        81.57 
TCGA-BS-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ 
       73.25        59.51        62.79        63.58        49.55        66.48 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV TCGA-D1-A0ZZ 
       19.79        29.95         4.87        28.67        23.93        22.55 
TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        1.74        21.99        39.48        30.08        29.88         1.91 
TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        31.07        10.65 
TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A17C 
        0.69         3.65        17.49        19.53         6.64         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       30.44         1.28        28.01         1.51         1.78        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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3JP 
       15.06         1.05         3.95         3.52        44.88        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       89.33        10.92        39.29        36.62        24.30        35.38 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-EC-A1NJ TCGA-EC-A24G 
       31.10        23.38        17.06         2.37        16.04        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        19.40        26.43        35.15        17.19        17.88 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH 
       16.34        14.53        24.89        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        11.08        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        14.14         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-JU-AAVI TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 
       96.69         7.76        18.21        23.24        15.45         7.00 
TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI 
       11.24        18.84        39.95        12.92        23.64        14.07 
TCGA-SJ-A6ZJ 
       18.28 

  AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE 
                       0.07                        0.20 
  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 
                      20.94                       24.30 
[1] "0.1 - 149.6 (20.9)" "0.2 - 191.8 (24.3)"
[1] "hr=" "2.3"
D5V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  5(1Q22) MUTATED                                       160
  AMP PEAK  5(1Q22) WILD-TYPE                                     235
                             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                                  79
  AMP PEAK  5(1Q22) WILD-TYPE                                33
D5V3, multiclass
                                         clus
vv                                        AMP PEAK  5(1Q22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                       160
  MIXED SEROUS AND ENDOMETRIOID                                  10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              79
                                         clus
vv                                        AMP PEAK  5(1Q22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         235
  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"
D5V4, binary
                             cls
clus                            0   1
  AMP PEAK  5(1Q22) MUTATED    62 187
  AMP PEAK  5(1Q22) WILD-TYPE  79 200
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q22) MUTATED     62  187
  AMP PEAK  5(1Q22) WILD-TYPE   79  200
     clus
vv    AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE
  NO                         62                          79
  YES                       187                         200
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(1Q22) MUTATED   168  11  12  16
  AMP PEAK  5(1Q22) WILD-TYPE 195  12   5  19
D5V5, multiclass
    clus
vv   AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE
  R0                       168                         195
  R1                        11                          12
  R2                        12                           5
  RX                        16                          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
  AMP PEAK  5(1Q22) MUTATED                                  2     5
  AMP PEAK  5(1Q22) WILD-TYPE                                2    15
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  5(1Q22) MUTATED                          59
  AMP PEAK  5(1Q22) WILD-TYPE                        42
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  5(1Q22) MUTATED                                           2   170
  AMP PEAK  5(1Q22) WILD-TYPE                                         7   196
D5V6, multiclass
                                           clus
vv                                          AMP PEAK  5(1Q22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  2
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                        59
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                           170
                                           clus
vv                                          AMP PEAK  5(1Q22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    2
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                          42
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             196
[1] 5 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     5 178
  AMP PEAK  5(1Q22) WILD-TYPE   9 189
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(1Q22) MUTATED      5  178
  AMP PEAK  5(1Q22) WILD-TYPE    9  189
                        clus
vv                       AMP PEAK  5(1Q22) MUTATED AMP PEAK  5(1Q22) WILD-TYPE
  HISPANIC OR LATINO                             5                           9
  NOT HISPANIC OR LATINO                       178                         189
[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   178  34
  AMP PEAK  6(1Q44) WILD-TYPE 279  35
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                        212                         314 
  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                         34                          35 
$`AMP PEAK  6(1Q44) MUTATED`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       36.69        10.29       149.56        83.51        17.85        32.78 
TCGA-A5-A0GG TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0GU 
       87.32        57.53        65.75        60.53        36.82        28.27 
TCGA-A5-A0GV TCGA-A5-A0GX TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       20.81        68.65        11.44        36.33         9.60         8.02 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A3BI TCGA-AJ-A3EJ 
       46.32        28.64        14.96        10.26        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OL 
       22.26        20.81        36.99        21.21        10.19        14.76 
TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A05D 
       16.87         0.13        83.67        21.99        23.31        57.80 
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-A0LH TCGA-AP-A0LI TCGA-AP-A0LL TCGA-AP-A0LO TCGA-AP-A1DM TCGA-AP-A1DO 
       36.36        97.71        83.97        33.40        55.89        31.30 
TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1E1 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       35.54        46.78        10.42        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A063 
        0.56        13.58        72.03        46.45        35.34        66.58 
TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A0IS TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A0J1 
       34.98        53.92        35.01        28.54        37.78        65.88 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        15.25        20.28        76.83        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH 
       67.50        11.08         4.77        40.80        81.37        17.75 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        2.96        64.93        43.82        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT 
        0.26         1.18        14.47         0.39        56.91        43.13 
TCGA-B5-A0JV TCGA-B5-A0K0 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       40.67        28.34        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A11R 
        4.11         8.71        75.72        36.82        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11Z TCGA-B5-A1MU TCGA-B5-A1MZ TCGA-B5-A3FH TCGA-B5-A3S1 
       27.35        17.36        50.89        15.29        14.27        29.65 
TCGA-B5-A5OC TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       41.06        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT 
       22.06        36.49        43.04        39.32        30.81        21.17 
TCGA-BG-A0MU TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0VV TCGA-BG-A0W1 TCGA-BG-A186 
       20.28        15.42        24.39        26.66        52.83        13.78 
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-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0U9 
       31.76        24.99        24.13        61.87        30.74        67.20 
TCGA-BS-A0UT TCGA-BS-A0V4 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       72.72        59.51        63.16        16.83         8.55         0.56 
TCGA-D1-A102 TCGA-D1-A160 TCGA-D1-A165 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A176 
        4.44         3.68         0.66        11.51        18.67        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       18.02         1.58         7.00        28.08        26.37        10.22 
TCGA-D1-A17R TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA 
       11.15        16.87        18.02        41.42         8.48         0.26 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-E6-A2P9 TCGA-EC-A1QX 
        4.11        16.93        27.16        16.31         6.67         7.36 
TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AZ TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GD 
       10.92        51.52        27.16         6.21         4.54        53.88 
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-A1GX TCGA-EY-A212 TCGA-EY-A214 
       15.09        16.11        12.43         6.48        10.19        14.40 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A549 TCGA-EY-A54A 
       20.05        45.76        31.04        11.38        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A3PV 
       16.96        41.06        39.95        59.01        28.96        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 
       45.01         1.74         7.76        14.04         2.43        13.28 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A917 TCGA-QS-A744 TCGA-QS-A8F1 
       26.10        23.97        12.92         6.97        14.83         4.44 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

$`AMP PEAK  6(1Q44) WILD-TYPE`
TCGA-2E-A9G8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH 
       41.06       106.88        37.02       112.54       105.37        74.10 
TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GW TCGA-A5-A0R6 TCGA-A5-A0R7 
       60.53        46.55        38.37        23.21        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-A23M TCGA-AJ-A23N 
       91.04         5.33         5.16         7.33         1.18        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
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        17.06 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3TW TCGA-AJ-A5DV 
       20.65        15.62        15.35        15.95        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A053 TCGA-AP-A056 TCGA-AP-A059 
       12.82        20.78         2.70         5.95        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0LG 
       63.91        45.53        36.89        23.87        12.20        63.16 
TCGA-AP-A0LJ TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP TCGA-AP-A0LQ TCGA-AP-A0LS 
       31.73        27.12        82.52        61.64        80.78        63.06 
TCGA-AP-A0LT TCGA-AP-A0LV TCGA-AP-A1DH TCGA-AP-A1DK TCGA-AP-A1DR TCGA-AP-A1DV 
       49.22        25.08        71.67        60.36        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E3 TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A062 
       30.90        27.85        19.82        29.69        68.35        45.99 
TCGA-AX-A06D TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IZ 
       12.26        51.09        27.39        30.02        60.66        43.82 
TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1CC TCGA-AX-A1CE 
       40.11        13.28        19.20        16.96        12.43        20.05 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC 
       25.12        36.39        30.12        71.24        61.18        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        19.36        26.33        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G9 TCGA-B5-A0JN 
        0.20         0.56         0.20         0.30        18.35        80.38 
TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 
       46.75        48.76        44.71        32.55        28.64        30.51 
TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       25.91        27.29        17.85       185.79       113.36        88.34 
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-A1MS TCGA-B5-A1MV 
       19.50        18.41        16.57       191.84       102.31        14.40 
TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        11.87        12.79       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       78.81        62.14        33.11        34.13        34.95        18.61 
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-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       43.30        16.34        34.29        52.64        56.58        14.83 
TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A18C TCGA-BG-A220 
       12.56        14.73        14.01        15.45        15.45        14.27 
TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB 
       20.02        23.70        20.12         6.81        34.98         6.21 
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-A0TJ TCGA-BS-A0U5 
       85.55        78.21         4.80        77.95        67.99        96.49 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UV 
       97.41        88.34        85.84        82.39        81.57        73.25 
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-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-A179 
        3.95         3.65        17.49        19.53         6.64        14.73 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17N TCGA-D1-A17Q 
        0.99        30.44         1.28        28.01         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.25         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DI-A1BU TCGA-DI-A1BY 
       44.88         4.27        89.33        10.92        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       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37        27.32        16.04 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       35.15        17.19        17.88        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GE TCGA-EY-A1GH TCGA-EY-A1GI 
       14.53        24.89        14.99        24.36        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1H0 
       23.90        13.97         6.90        15.81        11.08        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       12.59        18.87        22.82        29.10        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 
       17.92        14.14         5.88        40.01        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       13.84         8.98        96.69         9.07        28.93        25.02 
TCGA-FI-A2F9 TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       29.23        23.74         9.47        18.21        23.24        15.45 
TCGA-PG-A915 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR 
        7.00        11.24        18.84        39.95        12.92        23.64 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       14.07        18.28 

  AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE 
                       0.07                        0.20 
  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 
                     21.055                      23.885 
[1] "0.1 - 149.6 (21.1)" "0.2 - 191.8 (23.9)"
[1] "hr=" "1.5"
D6V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  6(1Q44) MUTATED                                       154
  AMP PEAK  6(1Q44) WILD-TYPE                                     241
                             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                                  51
  AMP PEAK  6(1Q44) WILD-TYPE                                61
D6V3, multiclass
                                         clus
vv                                        AMP PEAK  6(1Q44) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                       154
  MIXED SEROUS AND ENDOMETRIOID                                   8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              51
                                         clus
vv                                        AMP PEAK  6(1Q44) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         241
  MIXED SEROUS AND ENDOMETRIOID                                    13
  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"
D6V4, binary
                             cls
clus                            0   1
  AMP PEAK  6(1Q44) MUTATED    54 159
  AMP PEAK  6(1Q44) WILD-TYPE  87 228
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(1Q44) MUTATED     54  159
  AMP PEAK  6(1Q44) WILD-TYPE   87  228
     clus
vv    AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE
  NO                         54                          87
  YES                       159                         228
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  6(1Q44) MUTATED   146  10   9  11
  AMP PEAK  6(1Q44) WILD-TYPE 217  13   8  24
D6V5, multiclass
    clus
vv   AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE
  R0                       146                         217
  R1                        10                          13
  R2                         9                           8
  RX                        11                          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  6(1Q44) MUTATED                                  1     5
  AMP PEAK  6(1Q44) WILD-TYPE                                3    15
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  6(1Q44) MUTATED                          49
  AMP PEAK  6(1Q44) WILD-TYPE                        52
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  6(1Q44) MUTATED                                           2   150
  AMP PEAK  6(1Q44) WILD-TYPE                                         7   216
D6V6, multiclass
                                           clus
vv                                          AMP PEAK  6(1Q44) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                        49
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                           150
                                           clus
vv                                          AMP PEAK  6(1Q44) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                          52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             216
[1] 5 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     3 154
  AMP PEAK  6(1Q44) WILD-TYPE  11 213
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(1Q44) MUTATED      3  154
  AMP PEAK  6(1Q44) WILD-TYPE   11  213
                        clus
vv                       AMP PEAK  6(1Q44) MUTATED AMP PEAK  6(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             3                          11
  NOT HISPANIC OR LATINO                       154                         213
[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    89  28
  AMP PEAK  7(2P24.3) WILD-TYPE 368  41
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                          117                           409 
  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                           28                            41 
$`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 
       14.43        29.39        34.16         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05H 
        1.64        10.19        16.87        16.87        63.91        45.53 
TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IU 
       48.79        46.78        21.90        36.13        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 
       40.80        81.37        19.36        17.75         0.56         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-B5-A0JT TCGA-B5-A0JX TCGA-B5-A0K7 TCGA-B5-A0K9 
        0.30         0.26        43.13        44.71        17.10        11.01 
TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 
       75.72        50.89        12.79        29.65        19.33        20.94 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A18C 
       22.06        36.49        15.42        24.39        52.83        15.45 
TCGA-BG-A2AE TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD 
       23.70        11.31         6.81        35.90        24.13        16.64 
TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT TCGA-BS-A0UV TCGA-BS-A0V7 TCGA-BS-A0V8 
        4.80        61.87        72.72        73.25        63.58        49.55 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16S TCGA-D1-A17K 
       19.79        29.95        36.10        27.42        18.67        28.08 
TCGA-D1-A17R TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1BY TCGA-DI-A1NN 
       11.15         8.48         4.11        16.93        36.62        35.38 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A3B1 TCGA-EO-A3KU 
      110.10        48.36        27.32        49.15        26.96        22.26 
TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1GW 
        6.21        23.34         6.90        19.27        15.09        11.08 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D 
       10.19        14.40        29.10        11.38        14.70         5.88 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       41.06        39.95         7.99        28.93        25.02        41.06 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-PG-A7D5 
       45.01         7.76        14.04        23.74         9.47        23.97 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        7.00         4.44         0.07 

$`AMP PEAK  7(2P24.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW 
       57.53        60.53        46.55        38.37        36.82        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-A2K2 TCGA-A5-A2K5 
        7.92        11.44         9.60         8.02        91.04         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16         7.33        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       34.36         1.12        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       20.81        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        57.80        36.89        23.87        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-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-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-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC 
       13.28        19.20        13.55        15.25        20.28        12.43 
TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        76.83        72.56        54.12        25.12        36.39 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       71.24        61.18        34.32        46.49        26.33        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX 
        2.96        31.13        64.93         0.23         0.20        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20        20.52         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        80.38        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        27.29 
TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F 
       17.88        13.74        17.85         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-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-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.13        34.95        18.61        20.19        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-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        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-A2L7 TCGA-BK-A0CA TCGA-BK-A0CB 
        1.81         9.57        20.02        20.12        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-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-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-A0V4 TCGA-BS-A0V6 TCGA-BS-A0VI 
       85.84        82.39        81.57        59.51        62.79        63.16 
TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83         8.55         0.56         4.87        28.67 
TCGA-D1-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-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-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        37.32        36.36        37.51        36.79 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52        41.42        44.88         0.26         4.27 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1C3 
       89.33        10.92        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        16.04         7.36        16.80        10.92        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       27.16        17.88        16.34        14.53        24.89        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
        4.54        53.88        24.36        27.16        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       22.78        13.97        18.84        17.88        17.62        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-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
       17.92        14.14        19.89        16.96        40.01        39.88 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
       29.23         1.74         2.43        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        15.45        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE 
                         0.07                          0.13 
  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 
                        22.26                         23.38 
[1] "0.1 - 149.6 (22.3)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.6"
D7V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  7(2P24.3) MUTATED                                        54
  AMP PEAK  7(2P24.3) WILD-TYPE                                     341
                               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                                  57
  AMP PEAK  7(2P24.3) WILD-TYPE                                55
D7V3, multiclass
                                         clus
vv                                        AMP PEAK  7(2P24.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          54
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                57
                                         clus
vv                                        AMP PEAK  7(2P24.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           341
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                               cls
clus                              0   1
  AMP PEAK  7(2P24.3) MUTATED    22  96
  AMP PEAK  7(2P24.3) WILD-TYPE 119 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(2P24.3) MUTATED     22   96
  AMP PEAK  7(2P24.3) WILD-TYPE  119  291
     clus
vv    AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE
  NO                           22                           119
  YES                          96                           291
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(2P24.3) MUTATED    81   5   5  10
  AMP PEAK  7(2P24.3) WILD-TYPE 282  18  12  25
D7V5, multiclass
    clus
vv   AMP PEAK  7(2P24.3) MUTATED AMP PEAK  7(2P24.3) WILD-TYPE
  R0                          81                           282
  R1                           5                            18
  R2                           5                            12
  RX                          10                            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  7(2P24.3) MUTATED                                  0     3
  AMP PEAK  7(2P24.3) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  7(2P24.3) MUTATED                          22
  AMP PEAK  7(2P24.3) WILD-TYPE                        79
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  7(2P24.3) MUTATED                                           4    84
  AMP PEAK  7(2P24.3) WILD-TYPE                                         5   282
D7V6, multiclass
                                           clus
vv                                          AMP PEAK  7(2P24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          22
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              84
                                           clus
vv                                          AMP PEAK  7(2P24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            79
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               282
[1] 5 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  89
  AMP PEAK  7(2P24.3) WILD-TYPE  13 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(2P24.3) MUTATED      1   89
  AMP PEAK  7(2P24.3) WILD-TYPE   13  278
                        clus
vv                       AMP PEAK  7(2P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       AMP PEAK  7(2P24.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           278
[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    87  28
  AMP PEAK  8(2Q13) WILD-TYPE 370  41
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                        115                         411 
  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                         28                          41 
$`AMP PEAK  8(2Q13) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GN TCGA-A5-A0GV TCGA-A5-A0R6 
       36.69       149.56        37.02        60.53        20.81        19.96 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M 
       17.59        11.44        36.33        28.64        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A3BK TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW 
       14.43         1.68        22.26        20.81        10.19        16.87 
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        46.78 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A1CR TCGA-AX-A2H2 
       21.90        36.13        68.35        37.78        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IO 
       30.12        71.24        61.18        17.75         2.96        64.93 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K3 
        1.38         0.30         0.39        80.38        43.13        27.29 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A3S1 
       17.10        11.01         4.11        75.72        50.89        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M2 TCGA-BG-A0M6 TCGA-BG-A0RY TCGA-BG-A0VT 
       34.13        34.95        20.94        22.06        15.42        24.39 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       23.70         6.81        35.90        10.22        10.16        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0UT TCGA-BS-A0V7 TCGA-D1-A0ZO TCGA-D1-A0ZP 
       16.64         4.80        72.72        63.58        19.79        29.95 
TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NX 
       36.10        11.51        14.73        11.15        13.22        18.25 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN 
        8.48        44.88         0.26         4.11        16.93        35.38 
TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CG 
        9.37       110.10        48.36        27.32        10.92        51.42 
TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GC 
       19.40        26.96        22.26        16.34         6.21         4.54 
TCGA-EY-A1GH TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A214 
       23.34        23.90         6.90        19.27        15.09        14.40 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 
       29.10        13.84        11.38        14.70        41.06        39.95 
TCGA-FI-A2D4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
        7.99        25.02        29.23        41.06        45.01         7.76 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 
       14.04        23.74         9.47        18.21        23.97        12.92 
TCGA-QS-A8F1 
        4.44 

$`AMP PEAK  8(2Q13) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       41.06        10.29       106.88        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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-A0GW 
       60.53        46.55        38.37        36.82        28.27        23.21 
TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       68.65        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 
        7.92         9.60         8.02        91.04        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        5.16         7.33        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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        63.91 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        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-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-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-A2H7 
       72.56        54.12        67.50        25.12        36.39        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ 
       81.37        34.32        46.49        19.36        26.33        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        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-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J 
       17.85         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-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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        14.27        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       19.33        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-A0VV TCGA-BG-A0VW 
       39.32        30.81        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-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-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA 
        1.81         9.57        20.02        20.12        11.31        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 
        6.21        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-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-A0UV TCGA-BS-A0V4 TCGA-BS-A0V6 
       85.84        82.39        81.57        73.25        59.51        62.79 
TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN TCGA-D1-A0ZQ TCGA-D1-A0ZR 
       49.55        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-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-A17U 
       10.22         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41         0.72        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A3DG TCGA-DF-A2KV 
        1.05         3.95         3.52        41.42         4.27        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-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 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        51.52        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX 
       26.43        35.15        17.19        27.16        17.88        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI 
       24.89        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       22.78        13.97        18.84        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       10.19        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       27.35        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       40.01        39.88        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 
        9.07        28.93        28.96         1.74         2.43        13.28 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       26.10        23.24        15.45         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE 
                       0.26                        0.07 
  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 
                      20.94                       23.87 
[1] "0.3 - 149.6 (20.9)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.6"
D8V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  8(2Q13) MUTATED                                        44
  AMP PEAK  8(2Q13) WILD-TYPE                                     351
                             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                                  67
  AMP PEAK  8(2Q13) WILD-TYPE                                45
D8V3, multiclass
                                         clus
vv                                        AMP PEAK  8(2Q13) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        44
  MIXED SEROUS AND ENDOMETRIOID                                   5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              67
                                         clus
vv                                        AMP PEAK  8(2Q13) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         351
  MIXED SEROUS AND ENDOMETRIOID                                    16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                             cls
clus                            0   1
  AMP PEAK  8(2Q13) MUTATED    27  89
  AMP PEAK  8(2Q13) WILD-TYPE 114 298
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(2Q13) MUTATED     27   89
  AMP PEAK  8(2Q13) WILD-TYPE  114  298
     clus
vv    AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE
  NO                         27                         114
  YES                        89                         298
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  8(2Q13) MUTATED    76   5   7   9
  AMP PEAK  8(2Q13) WILD-TYPE 287  18  10  26
D8V5, multiclass
    clus
vv   AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE
  R0                        76                         287
  R1                         5                          18
  R2                         7                          10
  RX                         9                          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  8(2Q13) MUTATED                                  0     5
  AMP PEAK  8(2Q13) WILD-TYPE                                4    15
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK  8(2Q13) MUTATED                          30
  AMP PEAK  8(2Q13) WILD-TYPE                        71
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  8(2Q13) MUTATED                                           2    72
  AMP PEAK  8(2Q13) WILD-TYPE                                         7   294
D8V6, multiclass
                                           clus
vv                                          AMP PEAK  8(2Q13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  0
  ASIAN                                                             5
  BLACK OR AFRICAN AMERICAN                                        30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            72
                                           clus
vv                                          AMP PEAK  8(2Q13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    4
  ASIAN                                                              15
  BLACK OR AFRICAN AMERICAN                                          71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  WHITE                                                             294
[1] 5 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  77
  AMP PEAK  8(2Q13) WILD-TYPE  12 290
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  8(2Q13) MUTATED      2   77
  AMP PEAK  8(2Q13) WILD-TYPE   12  290
                        clus
vv                       AMP PEAK  8(2Q13) MUTATED AMP PEAK  8(2Q13) WILD-TYPE
  HISPANIC OR LATINO                             2                          12
  NOT HISPANIC OR LATINO                        77                         290
[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  18
  AMP PEAK  9(3P25.1) WILD-TYPE 395  51
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           80                           446 
  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                           18                            51 
$`AMP PEAK  9(3P25.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A2K2 
       36.69        37.02        65.75        36.82        36.33        91.04 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH 
       14.43         0.39        29.39        34.16        20.81        10.19 
TCGA-AJ-A3QS TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A0LF 
       16.87         0.13        63.91        36.89       125.42         3.39 
TCGA-AP-A0LH TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06B TCGA-AX-A06D 
       36.36        33.40        31.30        68.35        53.92        12.26 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
        4.77        30.12        40.80         0.30         0.26         0.39 
TCGA-B5-A0JN TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A3FB 
       80.38        17.88        33.50       191.84        11.87        78.81 
TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BS-A0U9 TCGA-BS-A0UV 
       34.95        34.98        15.42        52.83        67.20        73.25 
TCGA-BS-A0V8 TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 
       49.55        18.67        14.73        13.22        18.25         2.07 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A2QU TCGA-DI-A2QY 
       41.42         8.48        44.88         4.11        31.10       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A3AS 
       48.36        27.32        10.92        37.71        51.52        34.39 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       26.96        22.26         4.54        17.88        17.62        15.09 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A4KR TCGA-EY-A72D TCGA-FI-A2EW TCGA-FI-A2EX 
       11.08        10.19        11.38         5.88        59.01         9.07 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 
       25.02        29.23        45.01        14.04        23.97        12.92 
TCGA-PG-A915 TCGA-QS-A744 
        7.00        14.83 

$`AMP PEAK  9(3P25.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-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-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-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.96         1.18        10.26        19.79         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        22.26        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       12.82        20.78         2.70        83.67        21.99         5.95 
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        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91        48.79       117.99       110.37        63.16 
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        46.78        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        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 
       13.58        19.82        29.69        72.03        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        66.58        34.98        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-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-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 
       67.50        25.12        36.39        11.08        71.24        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 
        0.56        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        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        27.29        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-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-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       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-A3FC 
       11.70        15.29        12.79       116.25        96.30        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       33.11        14.27        29.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        22.06        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-A0VT TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       24.39        26.66        16.34        34.29        52.64        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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         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-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-A0VI TCGA-BS-A0WQ 
       72.72        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-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
        1.05         3.95         3.52         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-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        16.04         7.36        16.80        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       19.40        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
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-A1GT TCGA-EY-A1GU 
       13.97         6.90        19.27        18.84        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
       15.81         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        45.76        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        14.14        19.89        14.70        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR 
        8.98        96.69        28.93        28.96        41.06         1.74 
TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        7.76         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        15.45        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE 
                         0.13                          0.07 
  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 
                       27.140                        23.225 
[1] "0.1 - 191.8 (27.1)" "0.1 - 185.8 (23.2)"
[1] "hr=" "1.8"
D9V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK  9(3P25.1) MUTATED                                        36
  AMP PEAK  9(3P25.1) WILD-TYPE                                     359
                               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                                69
D9V3, multiclass
                                         clus
vv                                        AMP PEAK  9(3P25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          36
  MIXED SEROUS AND ENDOMETRIOID                                     1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                43
                                         clus
vv                                        AMP PEAK  9(3P25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           359
  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"
D9V4, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P25.1) MUTATED    15  65
  AMP PEAK  9(3P25.1) WILD-TYPE 126 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P25.1) MUTATED     15   65
  AMP PEAK  9(3P25.1) WILD-TYPE  126  322
     clus
vv    AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE
  NO                           15                           126
  YES                          65                           322
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(3P25.1) MUTATED    55   3   4   4
  AMP PEAK  9(3P25.1) WILD-TYPE 308  20  13  31
D9V5, multiclass
    clus
vv   AMP PEAK  9(3P25.1) MUTATED AMP PEAK  9(3P25.1) WILD-TYPE
  R0                          55                           308
  R1                           3                            20
  R2                           4                            13
  RX                           4                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(3P25.1) MUTATED                                  0     0
  AMP PEAK  9(3P25.1) WILD-TYPE                                4    20
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK  9(3P25.1) MUTATED                          23
  AMP PEAK  9(3P25.1) WILD-TYPE                        78
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK  9(3P25.1) MUTATED                                           4    47
  AMP PEAK  9(3P25.1) WILD-TYPE                                         5   319
D9V6, multiclass
                                           clus
vv                                          AMP PEAK  9(3P25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              47
                                           clus
vv                                          AMP PEAK  9(3P25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                20
  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"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(3P25.1) MUTATED     3  57
  AMP PEAK  9(3P25.1) WILD-TYPE  11 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(3P25.1) MUTATED      3   57
  AMP PEAK  9(3P25.1) WILD-TYPE   11  310
                        clus
vv                       AMP PEAK  9(3P25.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK  9(3P25.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           310
[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    46  17
  AMP PEAK 10(3P14.1) WILD-TYPE 411  52
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           63                           463 
  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                           17                            52 
$`AMP PEAK 10(3P14.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0R6 TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-AJ-A2QK TCGA-AJ-A3BD 
       36.69        19.96        91.04        28.64         0.39        34.16 
TCGA-AJ-A3EJ TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A05D TCGA-AP-A0LO 
        1.64        16.87        16.87         0.13        57.80        33.40 
TCGA-AP-A1DO TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HK 
       31.30        68.35        12.26        30.12        40.80         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A0K3 
       64.93         0.56         0.30         0.26         0.30        27.29 
TCGA-B5-A0K4 TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A3FB TCGA-B5-A5OD 
       17.88        33.50       191.84        11.87        78.81        34.13 
TCGA-BG-A0M4 TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BS-A0U9 TCGA-BS-A0UV 
       34.98        15.42        52.83        12.56        67.20        73.25 
TCGA-BS-A0V8 TCGA-D1-A16G TCGA-D1-A179 TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       49.55        27.42        14.73         2.07        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A8L9 
       44.88         4.27         4.11        12.39       110.10        27.32 
TCGA-EO-A22Y TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GQ TCGA-EY-A1GS 
       51.52        27.16        26.96         4.54        17.88        15.09 
TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2F9 
       11.08        10.19         5.88        41.06        59.01        29.23 
TCGA-FI-A3PX TCGA-QS-A744 TCGA-QS-A8F1 
       45.01        14.83         4.44 

$`AMP PEAK 10(3P14.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       36.82        28.27        20.81        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
       11.44        36.33         9.60         8.02        46.32         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        14.43        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79        29.39         2.40        34.36         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
       18.90         1.68        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-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-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        63.91        45.53        36.89        23.87        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-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-A1DQ TCGA-AP-A1DR 
       71.67        60.36        55.89        35.54        46.78        49.15 
TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       36.13         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-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-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-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       11.08         4.77        71.24        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.23         0.20        43.82         0.20        20.52         1.38 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        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-A0K6 TCGA-B5-A0K7 
       28.64        28.34        30.51        25.91        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-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-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.70        11.70        15.29        12.79       116.25        96.30 
TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       62.14        33.11        14.27        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 
       18.61        20.19        19.33        20.94        35.21        22.06 
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-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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         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-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-A0VI TCGA-BS-A0WQ 
       72.72        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-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DA 
       18.02        15.06         1.05         3.95         3.52         0.26 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30        35.38         9.37        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36        17.06         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       26.43        35.15        17.19        17.88        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        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-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        19.27        18.84        17.62        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
       15.81         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       22.82        20.05        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        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96        40.01        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        96.69         9.07        28.93        28.96        25.02 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.97        12.92         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       39.95        12.92        23.64        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE 
                         0.13                          0.07 
  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 
                        27.16                         23.31 
[1] "0.1 - 191.8 (27.2)" "0.1 - 185.8 (23.3)"
[1] "hr=" "2.4"
D10V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 10(3P14.1) MUTATED                                        33
  AMP PEAK 10(3P14.1) WILD-TYPE                                     362
                               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                                  27
  AMP PEAK 10(3P14.1) WILD-TYPE                                85
D10V3, multiclass
                                         clus
vv                                        AMP PEAK 10(3P14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          33
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                27
                                         clus
vv                                        AMP PEAK 10(3P14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           362
  MIXED SEROUS AND ENDOMETRIOID                                      18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED    10  53
  AMP PEAK 10(3P14.1) WILD-TYPE 131 334
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED     10   53
  AMP PEAK 10(3P14.1) WILD-TYPE  131  334
     clus
vv    AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  NO                           10                           131
  YES                          53                           334
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(3P14.1) MUTATED    39   5   3   3
  AMP PEAK 10(3P14.1) WILD-TYPE 324  18  14  32
D10V5, multiclass
    clus
vv   AMP PEAK 10(3P14.1) MUTATED AMP PEAK 10(3P14.1) WILD-TYPE
  R0                          39                           324
  R1                           5                            18
  R2                           3                            14
  RX                           3                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(3P14.1) MUTATED                                  1     0
  AMP PEAK 10(3P14.1) WILD-TYPE                                3    20
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 10(3P14.1) MUTATED                          15
  AMP PEAK 10(3P14.1) WILD-TYPE                        86
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 10(3P14.1) MUTATED                                           4    39
  AMP PEAK 10(3P14.1) WILD-TYPE                                         5   327
D10V6, multiclass
                                           clus
vv                                          AMP PEAK 10(3P14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          15
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              39
                                           clus
vv                                          AMP PEAK 10(3P14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                20
  BLACK OR AFRICAN AMERICAN                                            86
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  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"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(3P14.1) MUTATED     4  43
  AMP PEAK 10(3P14.1) WILD-TYPE  10 324
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(3P14.1) MUTATED      4   43
  AMP PEAK 10(3P14.1) WILD-TYPE   10  324
                        clus
vv                       AMP PEAK 10(3P14.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          43
                        clus
vv                       AMP PEAK 10(3P14.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           324
[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   137  34
  AMP PEAK 11(3Q26.2) WILD-TYPE 320  35
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                          171                           355 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                           34                            35 
$`AMP PEAK 11(3Q26.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OG 
       41.06        36.69        37.02        65.75        36.82        11.44 
TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M 
       36.33         8.02        91.04        46.32        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       14.43        29.39        34.16        18.90         1.64        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       17.06        20.81        15.62        16.87        16.87        20.78 
TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
        0.13        21.99         5.95        57.80        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO 
       48.79       125.42         3.39        97.71        33.40        31.30 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05W TCGA-AX-A06B TCGA-AX-A06D 
       46.78        36.13         0.56        68.35        53.92        12.26 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP 
       28.54        37.78        16.96        20.28        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       19.36         2.96        64.93         0.56        43.82        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN 
        1.38         0.30         0.26         0.30         0.39        80.38 
TCGA-B5-A0JX TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0KB TCGA-B5-A11H TCGA-B5-A11I 
       44.71        27.29        17.88         4.11        88.34        75.72 
TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FH TCGA-B5-A3S1 
       33.50       191.84        11.87        12.79        14.27        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT 
       34.13        34.95        34.98        22.06        36.49        21.17 
TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
       15.42        52.83        12.56         6.81        10.22        10.16 
TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A15V 
        4.80        67.20        73.25        49.55        29.95        39.48 
TCGA-D1-A168 TCGA-D1-A16G TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A176 TCGA-D1-A179 
       36.10        27.42        31.07        18.67        30.15        14.73 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G5 
       28.08        13.22         0.72        18.25         2.07        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN 
        8.48        44.88         0.26         4.11        16.93        35.38 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EC-A1QX 
        9.37        31.10       110.10        48.36        27.32         7.36 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS 
       10.92        49.15        37.71        51.52        51.42        34.39 
TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM 
       35.15        26.96        22.26        16.34        23.90         6.90 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW 
       19.27        17.88        17.62        15.09        15.81        11.08 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       10.19        14.40        20.05        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2EU 
       17.92        14.70         5.88        40.01        41.06        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01         9.07        28.93        25.02        41.06        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        1.74         7.76        14.04        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        23.97        12.92         7.00 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       14.83         4.44         0.07 

$`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 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
      112.54       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        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36         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        21.21        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A054 
       14.76        22.32        12.82         2.70        83.67        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        63.91        23.87        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-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-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-A1E4 TCGA-AP-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
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-A06F TCGA-AX-A06H TCGA-AX-A06J 
       45.99        66.58        34.98        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-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       19.20        13.55        15.25        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       54.12        67.50        25.12        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13         0.23         0.20 
TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.20         1.18        18.35        14.47        56.91        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-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       30.51        25.91        13.74        17.10        17.85        11.01 
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-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        36.82        32.09        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.40        14.70        11.70        15.29       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        33.11        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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        11.51        29.92        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KV 
       15.06         1.05         3.95         3.52         4.27        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       12.39        23.38        17.06         2.37         6.67        16.04 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX 
       19.40        26.43        17.19        27.16        17.88        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        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        14.14        19.89 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       16.96        39.88        39.95         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        29.23         2.43        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       18.84        39.95        12.92        23.64        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                         0.07                          0.20 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                       191.84                        185.79 
  AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE 
                        22.06                         23.47 
[1] "0.1 - 191.8 (22.1)" "0.2 - 185.8 (23.5)"
[1] "hr=" "2.2"
D11V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 11(3Q26.2) MUTATED                                        73
  AMP PEAK 11(3Q26.2) WILD-TYPE                                     322
                               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                                  90
  AMP PEAK 11(3Q26.2) WILD-TYPE                                22
D11V3, multiclass
                                         clus
vv                                        AMP PEAK 11(3Q26.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          73
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                90
                                         clus
vv                                        AMP PEAK 11(3Q26.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           322
  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    35 136
  AMP PEAK 11(3Q26.2) WILD-TYPE 106 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3Q26.2) MUTATED     35  136
  AMP PEAK 11(3Q26.2) WILD-TYPE  106  251
     clus
vv    AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE
  NO                           35                           106
  YES                         136                           251
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(3Q26.2) MUTATED   113   8   9  11
  AMP PEAK 11(3Q26.2) WILD-TYPE 250  15   8  24
D11V5, multiclass
    clus
vv   AMP PEAK 11(3Q26.2) MUTATED AMP PEAK 11(3Q26.2) WILD-TYPE
  R0                         113                           250
  R1                           8                            15
  R2                           9                             8
  RX                          11                            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 11(3Q26.2) MUTATED                                  0     3
  AMP PEAK 11(3Q26.2) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 11(3Q26.2) MUTATED                          52
  AMP PEAK 11(3Q26.2) WILD-TYPE                        49
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 11(3Q26.2) MUTATED                                           4   100
  AMP PEAK 11(3Q26.2) WILD-TYPE                                         5   266
D11V6, multiclass
                                           clus
vv                                          AMP PEAK 11(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          52
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                             100
                                           clus
vv                                          AMP PEAK 11(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            49
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  WHITE                                                               266
[1] 5 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     3 122
  AMP PEAK 11(3Q26.2) WILD-TYPE  11 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(3Q26.2) MUTATED      3  122
  AMP PEAK 11(3Q26.2) WILD-TYPE   11  245
                        clus
vv                       AMP PEAK 11(3Q26.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         122
                        clus
vv                       AMP PEAK 11(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           245
[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   128  31
  AMP PEAK 12(3Q26.2) WILD-TYPE 329  38
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                          159                           367 
  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                           31                            38 
$`AMP PEAK 12(3Q26.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A1OG 
       41.06        36.69        37.02        65.75        36.82        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        91.04        46.32        14.96         1.18        14.43 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       29.39        34.16         1.12        18.90         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A053 
       20.81        16.87        16.87         0.13        21.99         5.95 
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-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AW-A1PO 
       97.71        33.40        31.30        46.78        36.13         0.56 
TCGA-AX-A05W TCGA-AX-A06D TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF 
       68.35        12.26        37.78        16.96        20.28        76.83 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       36.39        11.08         4.77        30.12        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX 
       61.18        19.36         2.96        64.93         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN 
       20.52         1.38         0.30         0.26         0.39        80.38 
TCGA-B5-A0JX TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I 
       44.71        27.29        17.88         4.11         8.71        75.72 
TCGA-B5-A11R TCGA-B5-A1MR TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-B5-A5OE 
       33.50       191.84        11.87        12.79        34.13        34.95 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0RY TCGA-BG-A0W1 
       34.98        22.06        36.49        21.17        15.42        52.83 
TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0TE TCGA-BS-A0U9 
       12.56         6.81        10.22        10.16         4.80        67.20 
TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A15V TCGA-D1-A168 TCGA-D1-A16G 
       73.25        49.55        29.95        39.48        36.10        27.42 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A176 TCGA-D1-A17K TCGA-D1-A1NU 
       11.51        31.07        18.67        30.15        28.08        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        0.72        18.25        41.42         8.48        44.88         0.26 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ 
        4.11        16.93        35.38         9.37       110.10        48.36 
TCGA-E6-A8L9 TCGA-EC-A1QX TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y 
       27.32         7.36        10.92        49.15        37.71        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       51.42        34.39        26.96        22.26        16.34         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       23.90         6.90        19.27        17.88        17.62        15.09 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 
       15.81        11.08        10.19        14.40        20.05        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX 
       13.84        11.38        17.92        14.70         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       41.06        96.69        59.01         9.07        28.93        25.02 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 
       41.06        45.01         7.76        14.04        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
        9.47        26.10        23.24        23.97        12.92         7.00 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       14.83         4.44         0.07 

$`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 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
      112.54       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        10.26         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40        34.36         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 
       17.06        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        2.70        83.67        23.31        86.07         8.22        63.91 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.20        20.91       117.99       110.37        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-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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       27.85        16.24        21.90        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-A06F TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L TCGA-AX-A0IS 
       53.92        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-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        81.37        34.32        46.49        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       17.75        30.74        31.13         0.23         0.20         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        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-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       30.51        25.91        13.74        17.10        17.85        11.01 
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-A11S TCGA-B5-A11U TCGA-B5-A11V 
       40.50        36.82        32.09        27.35        16.73        19.56 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MS TCGA-B5-A1MU 
       19.50        18.41        17.36        16.57       102.31        50.89 
TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 TCGA-B5-A3FA 
       14.40        14.70        11.70        15.29       116.25        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M7 
       18.61        20.19        19.33        20.94        35.21        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-A0VT TCGA-BG-A0VV 
       43.04        39.32        30.81        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-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       34.98         6.21        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-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-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-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         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        3.52         4.27        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       39.29        36.62        24.30        12.39        31.10        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A24G TCGA-EO-A22R 
       17.06         2.37         6.67        16.04        16.80        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        17.19        27.16        17.88        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        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-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-A2OQ TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2D0 
       31.04        29.10        14.14        19.89        16.96        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F9 
       39.95         7.99        13.84         8.98        28.96        29.23 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        1.74         2.43        18.21        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       18.84        39.95        12.92        23.64        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE 
                         0.07                          0.20 
  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 
                        22.06                         23.47 
[1] "0.1 - 191.8 (22.1)" "0.2 - 185.8 (23.5)"
[1] "hr=" "2"  
D12V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 12(3Q26.2) MUTATED                                        65
  AMP PEAK 12(3Q26.2) WILD-TYPE                                     330
                               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                                  87
  AMP PEAK 12(3Q26.2) WILD-TYPE                                25
D12V3, multiclass
                                         clus
vv                                        AMP PEAK 12(3Q26.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          65
  MIXED SEROUS AND ENDOMETRIOID                                     7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                87
                                         clus
vv                                        AMP PEAK 12(3Q26.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           330
  MIXED SEROUS AND ENDOMETRIOID                                      14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                               cls
clus                              0   1
  AMP PEAK 12(3Q26.2) MUTATED    33 126
  AMP PEAK 12(3Q26.2) WILD-TYPE 108 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(3Q26.2) MUTATED     33  126
  AMP PEAK 12(3Q26.2) WILD-TYPE  108  261
     clus
vv    AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE
  NO                           33                           108
  YES                         126                           261
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 12(3Q26.2) MUTATED   105   8   9  10
  AMP PEAK 12(3Q26.2) WILD-TYPE 258  15   8  25
D12V5, multiclass
    clus
vv   AMP PEAK 12(3Q26.2) MUTATED AMP PEAK 12(3Q26.2) WILD-TYPE
  R0                         105                           258
  R1                           8                            15
  R2                           9                             8
  RX                          10                            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 12(3Q26.2) MUTATED                                  0     3
  AMP PEAK 12(3Q26.2) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 12(3Q26.2) MUTATED                          48
  AMP PEAK 12(3Q26.2) WILD-TYPE                        53
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 12(3Q26.2) MUTATED                                           4    93
  AMP PEAK 12(3Q26.2) WILD-TYPE                                         5   273
D12V6, multiclass
                                           clus
vv                                          AMP PEAK 12(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          48
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           4
  WHITE                                                              93
                                           clus
vv                                          AMP PEAK 12(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            53
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             5
  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"
D12V7, binary
                               cls
clus                              0   1
  AMP PEAK 12(3Q26.2) MUTATED     2 114
  AMP PEAK 12(3Q26.2) WILD-TYPE  12 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 12(3Q26.2) MUTATED      2  114
  AMP PEAK 12(3Q26.2) WILD-TYPE   12  253
                        clus
vv                       AMP PEAK 12(3Q26.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       AMP PEAK 12(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           253
[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    42  10
  AMP PEAK 13(4P16.3) WILD-TYPE 415  59
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           52                           474 
  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                           10                            59 
$`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        14.43        29.39 
TCGA-AJ-A3BF TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
        1.12        63.91        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         0.56         1.38        80.38        29.65        34.13 
TCGA-BG-A0M6 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A0ZZ TCGA-D1-A16I 
       22.06        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 
      110.10        10.92        37.71        51.42        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        11.08        29.10         5.88 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-KP-A3W4 TCGA-PG-A914 
       96.69        29.23        18.21        12.92 

$`AMP PEAK 13(4P16.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92        36.33         9.60         8.02        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.33         5.16         7.33        14.96        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
       19.79         2.40        34.36        34.16         0.76        18.90 
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        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        12.20        20.91       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        46.78 
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 
       21.90        36.13         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-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-A1CP TCGA-AX-A1CR 
       20.05        72.56        54.12        67.50        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 
        0.23         0.20        43.82         0.20        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        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        27.29 
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-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OE 
       78.81        62.14        33.11        14.27        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-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        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98         6.21        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-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-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         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-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-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        8.48         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
        9.37        12.39        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        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
       53.88        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-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       45.76        31.04        27.35        13.84        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       14.14        19.89        14.70        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       39.88        39.95         7.99        13.84         8.98        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-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
        1.74         7.76        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 
        9.47        26.10        23.24        15.45        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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE 
                         0.56                          0.07 
  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 
                       23.225                        23.340 
[1] "0.6 - 125.4 (23.2)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.5"
D13V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 13(4P16.3) MUTATED                                        15
  AMP PEAK 13(4P16.3) WILD-TYPE                                     380
                               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                                  36
  AMP PEAK 13(4P16.3) WILD-TYPE                                76
D13V3, multiclass
                                         clus
vv                                        AMP PEAK 13(4P16.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          15
  MIXED SEROUS AND ENDOMETRIOID                                     1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                36
                                         clus
vv                                        AMP PEAK 13(4P16.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           380
  MIXED SEROUS AND ENDOMETRIOID                                      20
  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"
D13V4, binary
                               cls
clus                              0   1
  AMP PEAK 13(4P16.3) MUTATED    16  36
  AMP PEAK 13(4P16.3) WILD-TYPE 125 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4P16.3) MUTATED     16   36
  AMP PEAK 13(4P16.3) WILD-TYPE  125  351
     clus
vv    AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE
  NO                           16                           125
  YES                          36                           351
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 13(4P16.3) MUTATED    35   3   4   2
  AMP PEAK 13(4P16.3) WILD-TYPE 328  20  13  33
D13V5, multiclass
    clus
vv   AMP PEAK 13(4P16.3) MUTATED AMP PEAK 13(4P16.3) WILD-TYPE
  R0                          35                           328
  R1                           3                            20
  R2                           4                            13
  RX                           2                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(4P16.3) MUTATED                                  0     2
  AMP PEAK 13(4P16.3) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 13(4P16.3) MUTATED                          13
  AMP PEAK 13(4P16.3) WILD-TYPE                        88
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 13(4P16.3) MUTATED                                           0    30
  AMP PEAK 13(4P16.3) WILD-TYPE                                         9   336
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                                                              30
                                           clus
vv                                          AMP PEAK 13(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            88
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               336
[1] 5 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  32
  AMP PEAK 13(4P16.3) WILD-TYPE  12 335
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 13(4P16.3) MUTATED      2   32
  AMP PEAK 13(4P16.3) WILD-TYPE   12  335
                        clus
vv                       AMP PEAK 13(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       AMP PEAK 13(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           335
[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  21
  AMP PEAK 14(5P15.33) WILD-TYPE 391  48
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            87                            439 
  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                            21                             48 
$`AMP PEAK 14(5P15.33) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GB TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LP 
       36.69        37.02        32.78        65.75        36.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
       14.43         0.39        22.26        20.81        10.19        16.87 
TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI 
       16.87        45.53        48.79       125.42        36.36        97.71 
TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A2H2 
       31.30        46.78         0.56        35.01        37.78         4.77 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       71.24        61.18         2.96         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A1MY TCGA-B5-A3FD TCGA-B5-A5OD 
        0.30         0.39        80.38        11.87        33.11        34.13 
TCGA-B5-A5OE TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A3PP 
       34.95        35.21        22.06        24.39        15.45         6.81 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0V8 TCGA-D1-A15V 
       10.22        10.16        24.13         4.80        49.55        39.48 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3DH 
       31.07        14.73        13.22         0.72        18.25         4.11 
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       110.10        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU 
       27.32        10.92        37.71        51.42        26.96        22.26 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A2ON TCGA-EY-A3QX 
        4.54        23.90        17.62        15.09        20.05        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX 
       11.38        17.92         5.88        39.95        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ 
       28.93        25.02         1.74         7.76        14.04        23.74 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       12.92         7.00         4.44 

$`AMP PEAK 14(5P15.33) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
      112.54       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-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        7.33         1.18        10.26        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        20.91       117.99       110.37 
TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN 
        3.39        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-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-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
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-A0IU TCGA-AX-A0IZ 
       51.09        27.39        30.02        60.66        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-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-A2H4 
       54.12        67.50        25.12        36.39        11.08        30.12 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       40.80        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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 
       27.29        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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW 
       78.81        62.14        14.27        29.65        41.06        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.19        19.33        20.94        34.98        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-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        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
       11.31        35.90        34.98         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-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-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-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-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
        2.33        22.92         1.41        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-E6-A1LX 
       27.16        16.31        39.29        36.62        24.30        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        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       27.16        17.88        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-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-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO 
       12.59        10.19        14.40        18.87        22.82        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       31.04        29.10        27.35        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        8.98        96.69        28.96        29.23        41.06        45.01 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        23.97        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       12.92        23.64        14.83        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE 
                          0.20                           0.07 
  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 
                         20.81                          23.47 
[1] "0.2 - 125.4 (20.8)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.5"
D14V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 14(5P15.33) MUTATED                                        30
  AMP PEAK 14(5P15.33) WILD-TYPE                                     365
                                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                                  55
  AMP PEAK 14(5P15.33) WILD-TYPE                                57
D14V3, multiclass
                                         clus
vv                                        AMP PEAK 14(5P15.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           30
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 55
                                         clus
vv                                        AMP PEAK 14(5P15.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            365
  MIXED SEROUS AND ENDOMETRIOID                                       18
  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"
D14V4, binary
                                cls
clus                               0   1
  AMP PEAK 14(5P15.33) MUTATED    17  71
  AMP PEAK 14(5P15.33) WILD-TYPE 124 316
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(5P15.33) MUTATED     17   71
  AMP PEAK 14(5P15.33) WILD-TYPE  124  316
     clus
vv    AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE
  NO                            17                            124
  YES                           71                            316
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(5P15.33) MUTATED    57   3   6   8
  AMP PEAK 14(5P15.33) WILD-TYPE 306  20  11  27
D14V5, multiclass
    clus
vv   AMP PEAK 14(5P15.33) MUTATED AMP PEAK 14(5P15.33) WILD-TYPE
  R0                           57                            306
  R1                            3                             20
  R2                            6                             11
  RX                            8                             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 14(5P15.33) MUTATED                                  1     2
  AMP PEAK 14(5P15.33) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 14(5P15.33) MUTATED                          30
  AMP PEAK 14(5P15.33) WILD-TYPE                        71
                                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      49
  AMP PEAK 14(5P15.33) WILD-TYPE   317
D14V6, multiclass
                                           clus
vv                                          AMP PEAK 14(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               49
                                           clus
vv                                          AMP PEAK 14(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             71
  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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(5P15.33) MUTATED     4  62
  AMP PEAK 14(5P15.33) WILD-TYPE  10 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(5P15.33) MUTATED      4   62
  AMP PEAK 14(5P15.33) WILD-TYPE   10  305
                        clus
vv                       AMP PEAK 14(5P15.33) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           62
                        clus
vv                       AMP PEAK 14(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            305
[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    41  11
  AMP PEAK 15(5Q35.3) WILD-TYPE 416  58
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           52                           474 
  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                           11                            58 
$`AMP PEAK 15(5Q35.3) MUTATED`
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A6NU 
       14.43        29.39         1.12        10.19        16.87        20.78 
TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A1DO TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IS 
        5.95        57.80        31.30        21.90        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         0.56        20.52 
TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M6 
        1.38         0.39        80.38        11.87        12.79        22.06 
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-JU-AAVI 
       14.70        96.69        59.01        29.23         1.74         7.76 
TCGA-K6-A3WQ TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A8F1 
       14.04        23.97        12.92         4.44 

$`AMP PEAK 15(5Q35.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        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-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        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-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        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16         0.76        18.90         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        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87        22.32        12.82         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        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       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-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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       55.89        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         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-A0IU TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        28.54        37.78        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-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        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX 
        2.96        31.13        64.93         0.23         0.20        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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 
       27.29        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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-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-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 
       20.02        23.70        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        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-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-A16I TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-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-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-A3DH TCGA-D1-A3JP 
       41.42         8.48        44.88         0.26         4.11        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       24.30         9.37        12.39        31.10       110.10        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        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       46.26        57.60        51.52        51.42        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.88        16.11        12.43        15.81        11.08         6.48 
TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       19.33        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       45.76        31.04        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY 
       39.95         7.99        13.84         8.98         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       28.96        25.02        41.06        45.01         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE 
                         0.39                          0.07 
  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 
                       16.160                        23.805 
[1] "0.4 - 96.7 (16.2)"  "0.1 - 191.8 (23.8)"
[1] "hr=" "2.4"
D15V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 15(5Q35.3) MUTATED                                        20
  AMP PEAK 15(5Q35.3) WILD-TYPE                                     375
                               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                                  31
  AMP PEAK 15(5Q35.3) WILD-TYPE                                81
D15V3, multiclass
                                         clus
vv                                        AMP PEAK 15(5Q35.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          20
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                31
                                         clus
vv                                        AMP PEAK 15(5Q35.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           375
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                               cls
clus                              0   1
  AMP PEAK 15(5Q35.3) MUTATED    10  43
  AMP PEAK 15(5Q35.3) WILD-TYPE 131 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5Q35.3) MUTATED     10   43
  AMP PEAK 15(5Q35.3) WILD-TYPE  131  344
     clus
vv    AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE
  NO                           10                           131
  YES                          43                           344
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 15(5Q35.3) MUTATED    33   3   3   3
  AMP PEAK 15(5Q35.3) WILD-TYPE 330  20  14  32
D15V5, multiclass
    clus
vv   AMP PEAK 15(5Q35.3) MUTATED AMP PEAK 15(5Q35.3) WILD-TYPE
  R0                          33                           330
  R1                           3                            20
  R2                           3                            14
  RX                           3                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(5Q35.3) MUTATED                                  0     1
  AMP PEAK 15(5Q35.3) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 15(5Q35.3) MUTATED                          20
  AMP PEAK 15(5Q35.3) WILD-TYPE                        81
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 15(5Q35.3) MUTATED                                           0    30
  AMP PEAK 15(5Q35.3) WILD-TYPE                                         9   336
D15V6, multiclass
                                           clus
vv                                          AMP PEAK 15(5Q35.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              30
                                           clus
vv                                          AMP PEAK 15(5Q35.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               336
[1] 5 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  45
  AMP PEAK 15(5Q35.3) WILD-TYPE  14 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 15(5Q35.3) MUTATED      0   45
  AMP PEAK 15(5Q35.3) WILD-TYPE   14  322
                        clus
vv                       AMP PEAK 15(5Q35.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       AMP PEAK 15(5Q35.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           322
[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  22
  AMP PEAK 16(6P24.2) WILD-TYPE 365  47
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                          114                           412 
  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                           22                            47 
$`AMP PEAK 16(6P24.2) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GR TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       36.69        37.02        36.82        11.44        36.33        91.04 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI 
       14.96         1.18        14.43        34.16         1.12        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW 
        1.64        20.81        10.19        16.87        16.87         0.13 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
        5.95        63.91        57.80        45.53        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A06J 
       97.71        33.40        46.78        36.13        53.92        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-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G1 
       30.12        40.80        81.37        64.93        43.82        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0K3 
        1.38         0.26         0.39        80.38        46.75        27.29 
TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU 
       17.85         8.71        75.72        33.50        27.35        50.89 
TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 
       12.79        78.81        29.65        34.13        34.95        36.49 
TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       15.45        35.90        10.22        24.13        16.64        67.20 
TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A1NW 
       49.55        36.10        31.07        18.67        14.73         0.72 
TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KY TCGA-DI-A1NN 
        2.07        41.42         4.27         4.11        10.92        35.38 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
       31.10       110.10        27.32        37.71        51.52        51.42 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GQ 
       26.96        22.26        16.34         4.54        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       17.62        10.19        14.40        20.05        29.10        27.35 
TCGA-EY-A3QX TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       13.84        40.01        39.88        39.95        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ 
        9.07        28.93        25.02        29.23        45.01        14.04 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       26.10        23.97        12.92         7.00         4.44         0.07 

$`AMP PEAK 16(6P24.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-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 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.76         1.68        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       14.76        22.32        12.82        20.78         2.70        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N 
       21.99        23.31        86.07         8.22        36.89        23.87 
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-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        21.90         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-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-A1CI 
       13.28        19.20        13.55        15.25        20.05        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-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74         2.96        31.13         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.30         0.30         1.18        18.35        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-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H 
       17.10        11.01         4.11       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-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
       15.29       116.25        96.30        62.14        33.11        14.27 
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        22.06        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        20.02        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         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JP 
        3.95         3.52         8.48        44.88         0.26        16.93 
TCGA-DF-A2KV TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       89.33        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        12.39        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH 
       61.74        61.55        66.90        46.26        57.60        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        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-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
        6.90        18.84        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 
       11.08         6.48        19.33        12.59        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        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D4 TCGA-FI-A2D5 
       14.70        16.96         5.88        41.06         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 
        8.98        28.96        41.06         1.74         7.76         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       23.74        13.28         9.47        18.21        23.24        15.45 
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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        14.07        18.28         0.23 

  AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE 
                         0.07                          0.20 
  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 
                       27.335                        22.665 
[1] "0.1 - 125.4 (27.3)" "0.2 - 191.8 (22.7)"
[1] "hr=" "1.6"
D16V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 16(6P24.2) MUTATED                                        45
  AMP PEAK 16(6P24.2) WILD-TYPE                                     350
                               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                                  64
  AMP PEAK 16(6P24.2) WILD-TYPE                                48
D16V3, multiclass
                                         clus
vv                                        AMP PEAK 16(6P24.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          45
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                64
                                         clus
vv                                        AMP PEAK 16(6P24.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           350
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D16V4, binary
                               cls
clus                              0   1
  AMP PEAK 16(6P24.2) MUTATED    23  91
  AMP PEAK 16(6P24.2) WILD-TYPE 118 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(6P24.2) MUTATED     23   91
  AMP PEAK 16(6P24.2) WILD-TYPE  118  296
     clus
vv    AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE
  NO                           23                           118
  YES                          91                           296
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 16(6P24.2) MUTATED    73   5   5   8
  AMP PEAK 16(6P24.2) WILD-TYPE 290  18  12  27
D16V5, multiclass
    clus
vv   AMP PEAK 16(6P24.2) MUTATED AMP PEAK 16(6P24.2) WILD-TYPE
  R0                          73                           290
  R1                           5                            18
  R2                           5                            12
  RX                           8                            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 16(6P24.2) MUTATED                                  0     2
  AMP PEAK 16(6P24.2) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 16(6P24.2) MUTATED                          30
  AMP PEAK 16(6P24.2) WILD-TYPE                        71
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 16(6P24.2) MUTATED                                           2    74
  AMP PEAK 16(6P24.2) WILD-TYPE                                         7   292
D16V6, multiclass
                                           clus
vv                                          AMP PEAK 16(6P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              74
                                           clus
vv                                          AMP PEAK 16(6P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  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"
D16V7, binary
                               cls
clus                              0   1
  AMP PEAK 16(6P24.2) MUTATED     2  76
  AMP PEAK 16(6P24.2) WILD-TYPE  12 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 16(6P24.2) MUTATED      2   76
  AMP PEAK 16(6P24.2) WILD-TYPE   12  291
                        clus
vv                       AMP PEAK 16(6P24.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          76
                        clus
vv                       AMP PEAK 16(6P24.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           291
[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    88  16
  AMP PEAK 17(6P22.3) WILD-TYPE 369  53
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                          104                           422 
  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                           16                            53 
$`AMP PEAK 17(6P22.3) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LP 
       36.69        37.02        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-A3IA 
        1.18        14.43        34.16         1.12        18.90        20.81 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A05D 
       10.19        16.87        16.87        20.78         0.13        57.80 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ TCGA-AP-A5FX 
       48.79       125.42        97.71        33.40        46.78        36.13 
TCGA-AX-A06J TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       30.02        37.78        16.96        20.28        12.43        76.83 
TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G6 
       11.08        40.80        81.37        20.52         1.38         0.26 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E 
        0.39        80.38        46.75        17.85         4.11         8.71 
TCGA-B5-A11I TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3S1 
       75.72        33.50        27.35        50.89        12.79        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A0C9 TCGA-BK-A0CC 
       34.13        34.95        36.49        15.45        35.90        10.22 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A168 TCGA-D1-A16N 
       24.13        16.64        67.20        49.55        36.10        31.07 
TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G5 TCGA-D1-A3DG TCGA-D1-A3DH 
       18.67        13.22         0.72        41.42         4.27         4.11 
TCGA-DF-A2KY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y8 
       10.92        35.38         9.37       110.10        27.32        37.71 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       51.52        51.42        26.96        22.26        16.34         4.54 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A210 TCGA-EY-A212 
       19.27        17.88        17.62        15.09        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2CX 
       14.40        20.05        29.10        27.35        13.84        40.01 
TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PX 
       39.88        59.01         9.07        28.93        29.23        45.01 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
        7.76        14.04        26.10        23.97        12.92         7.00 
TCGA-QS-A8F1 TCGA-SL-A6J9 
        4.44         0.07 

$`AMP PEAK 17(6P22.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        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        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36         0.76         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        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.35        15.95        14.76        22.32        12.82         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-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        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        21.90         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-A06L 
       34.98        53.92        12.26        51.09        27.39        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-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       19.20        13.55        15.25        20.05        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-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.56        43.82         0.20         0.30         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       18.35        14.47        56.91        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-A11F 
       27.29        17.88        13.74        17.10        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-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       36.82        32.09        16.73        19.56        19.50        18.41 
TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        14.27        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        22.06        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        20.02        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         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KZ 
        8.48        44.88         0.26        16.93        89.33        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU 
       16.31        39.29        36.62        24.30        12.39        31.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        17.19        27.16        17.88        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        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-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         6.48        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 
       18.87        22.82        45.76        31.04        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY 
       14.14        19.89        14.70        16.96         5.88        41.06 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 
       39.95         7.99        13.84         8.98        96.69        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       25.02        41.06         1.74         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        9.47        18.21        23.24        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE 
                         0.07                          0.20 
  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 
                       21.535                        23.360 
[1] "0.1 - 125.4 (21.5)" "0.2 - 191.8 (23.4)"
[1] "hr=" "1.3"
D17V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 17(6P22.3) MUTATED                                        40
  AMP PEAK 17(6P22.3) WILD-TYPE                                     355
                               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                                  60
  AMP PEAK 17(6P22.3) WILD-TYPE                                52
D17V3, multiclass
                                         clus
vv                                        AMP PEAK 17(6P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          40
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                60
                                         clus
vv                                        AMP PEAK 17(6P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           355
  MIXED SEROUS AND ENDOMETRIOID                                      17
  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"
D17V4, binary
                               cls
clus                              0   1
  AMP PEAK 17(6P22.3) MUTATED    21  83
  AMP PEAK 17(6P22.3) WILD-TYPE 120 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(6P22.3) MUTATED     21   83
  AMP PEAK 17(6P22.3) WILD-TYPE  120  304
     clus
vv    AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE
  NO                           21                           120
  YES                          83                           304
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 17(6P22.3) MUTATED    66   4   5   8
  AMP PEAK 17(6P22.3) WILD-TYPE 297  19  12  27
D17V5, multiclass
    clus
vv   AMP PEAK 17(6P22.3) MUTATED AMP PEAK 17(6P22.3) WILD-TYPE
  R0                          66                           297
  R1                           4                            19
  R2                           5                            12
  RX                           8                            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 17(6P22.3) MUTATED                                  0     2
  AMP PEAK 17(6P22.3) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 17(6P22.3) MUTATED                          33
  AMP PEAK 17(6P22.3) WILD-TYPE                        68
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 17(6P22.3) MUTATED                                           2    62
  AMP PEAK 17(6P22.3) WILD-TYPE                                         7   304
D17V6, multiclass
                                           clus
vv                                          AMP PEAK 17(6P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          33
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              62
                                           clus
vv                                          AMP PEAK 17(6P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            68
  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"
D17V7, binary
                               cls
clus                              0   1
  AMP PEAK 17(6P22.3) MUTATED     1  71
  AMP PEAK 17(6P22.3) WILD-TYPE  13 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 17(6P22.3) MUTATED      1   71
  AMP PEAK 17(6P22.3) WILD-TYPE   13  296
                        clus
vv                       AMP PEAK 17(6P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          71
                        clus
vv                       AMP PEAK 17(6P22.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           296
[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  15
  AMP PEAK 18(6Q25.1) WILD-TYPE 388  54
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           84                           442 
  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                           15                            54 
$`AMP PEAK 18(6Q25.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QN TCGA-AJ-A3BI TCGA-AJ-A3EM 
       36.69        14.96         1.18         2.40        18.90        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A8CW TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A0LO 
       20.81        10.19         0.13        48.79        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06J TCGA-AX-A1CC TCGA-AX-A2H4 TCGA-AX-A2H7 
       46.78        36.13        30.02        12.43        30.12        40.80 
TCGA-AX-A2HA TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3GI TCGA-B5-A0JN 
       81.37         0.56        43.82        20.52         0.39        80.38 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11I TCGA-B5-A11R 
       27.29        17.85         4.11         8.71        75.72        33.50 
TCGA-B5-A1N2 TCGA-B5-A3FB TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 TCGA-BG-A18C 
       12.79        78.81        29.65        34.13        36.49        15.45 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI 
       35.90        10.22        10.16        24.13        16.64        61.87 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A16S 
       67.20        49.55         8.55        36.10        11.51        18.67 
TCGA-D1-A17K TCGA-D1-A2G5 TCGA-DI-A1NN TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22X 
       28.08        41.42        35.38        10.92        49.15        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ 
       51.52        51.42        22.26        16.34         4.54        23.90 
TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 
       19.27        17.88        17.62        15.09        15.81        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A 
       14.40        20.05        27.35        13.84        11.38        14.70 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 
       40.01        39.88        59.01         9.07        25.02        29.23 
TCGA-FI-A3PX TCGA-KP-A3VZ TCGA-PG-A5BC TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       45.01        23.74        23.24         7.00         4.44         0.07 

$`AMP PEAK 18(6Q25.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N 
       46.32        28.64         5.33         5.16         7.33        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26         0.39        19.79        29.39        34.36        34.16 
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-A3OJ 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.95        14.76        16.87        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A054 
       20.78         2.70        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        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       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-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        21.90 
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-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-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-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
        4.77        71.24        61.18        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.23         0.20         0.20         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        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-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11L 
       11.01       185.79       113.36        88.34        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-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-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH 
       15.29       116.25        96.30        62.14        33.11        14.27 
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-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
        6.81        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-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-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79        29.95         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-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       15.72        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW 
       24.30         2.33        22.92         1.41        13.22         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52         8.48        44.88         0.26         4.27 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.11        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30         9.37        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
      110.10        23.38        48.36        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R 
       27.32        16.04         7.36        16.80        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       61.55        66.90        46.26        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX 
       35.15        17.19        27.16        17.88        26.96        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        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-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        11.08         6.48        19.33        12.59 
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-A2CY TCGA-FI-A2D2 
       14.14        19.89        16.96         5.88        41.06        39.95 
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-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 
       41.06         1.74         7.76        14.04         2.43        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        9.47        26.10        18.21        15.45        23.97        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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        14.07        18.28         0.23 

  AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE 
                         0.07                          0.20 
  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 
                        22.75                         23.36 
[1] "0.1 - 97.7 (22.8)"  "0.2 - 191.8 (23.4)"
[1] "hr=" "1.6"
D18V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 18(6Q25.1) MUTATED                                        44
  AMP PEAK 18(6Q25.1) WILD-TYPE                                     351
                               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                                  38
  AMP PEAK 18(6Q25.1) WILD-TYPE                                74
D18V3, multiclass
                                         clus
vv                                        AMP PEAK 18(6Q25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          44
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                38
                                         clus
vv                                        AMP PEAK 18(6Q25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           351
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                               cls
clus                              0   1
  AMP PEAK 18(6Q25.1) MUTATED    19  65
  AMP PEAK 18(6Q25.1) WILD-TYPE 122 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(6Q25.1) MUTATED     19   65
  AMP PEAK 18(6Q25.1) WILD-TYPE  122  322
     clus
vv    AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE
  NO                           19                           122
  YES                          65                           322
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 18(6Q25.1) MUTATED    52   1   4   8
  AMP PEAK 18(6Q25.1) WILD-TYPE 311  22  13  27
D18V5, multiclass
    clus
vv   AMP PEAK 18(6Q25.1) MUTATED AMP PEAK 18(6Q25.1) WILD-TYPE
  R0                          52                           311
  R1                           1                            22
  R2                           4                            13
  RX                           8                            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 18(6Q25.1) MUTATED                                  0     1
  AMP PEAK 18(6Q25.1) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 18(6Q25.1) MUTATED                          28
  AMP PEAK 18(6Q25.1) WILD-TYPE                        73
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 18(6Q25.1) MUTATED                                           2    48
  AMP PEAK 18(6Q25.1) WILD-TYPE                                         7   318
D18V6, multiclass
                                           clus
vv                                          AMP PEAK 18(6Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              48
                                           clus
vv                                          AMP PEAK 18(6Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  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"
D18V7, binary
                               cls
clus                              0   1
  AMP PEAK 18(6Q25.1) MUTATED     1  57
  AMP PEAK 18(6Q25.1) WILD-TYPE  13 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(6Q25.1) MUTATED      1   57
  AMP PEAK 18(6Q25.1) WILD-TYPE   13  310
                        clus
vv                       AMP PEAK 18(6Q25.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK 18(6Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           310
[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    66  23
  AMP PEAK 19(7Q31.2) WILD-TYPE 391  46
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           89                           437 
  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                           23                            46 
$`AMP PEAK 19(7Q31.2) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GV TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A2QN 
       41.06        20.81        36.33        28.64        14.96         2.40 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3QS 
        1.12        18.90         1.64        20.81        15.62        16.87 
TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A053 TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       16.87        20.78         5.95        48.79       125.42         3.39 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AX-A05W TCGA-AX-A1C8 
       36.36        97.71        33.40        21.90        68.35        13.55 
TCGA-AX-A1C9 TCGA-AX-A2H4 TCGA-AX-A2HJ TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       15.25        30.12        30.74         0.20        20.52         1.38 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K0 TCGA-B5-A0K4 
        0.26         0.39        56.91        43.13        28.34        17.88 
TCGA-B5-A0KB TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-BG-A0M3 TCGA-BG-A0M8 
        4.11       102.31        50.89        14.40        35.21        36.49 
TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A0C9 
       30.81        15.42        24.39        15.45        23.70        35.90 
TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0UT TCGA-D1-A0ZN TCGA-D1-A16I 
       16.64         4.80        61.87        72.72        16.83        11.51 
TCGA-D1-A17C TCGA-D1-A17R TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A2G6 TCGA-D1-A3JP 
        0.99        11.15         0.72        16.87         8.48        16.93 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A22Y 
        9.37        31.10        27.32        16.04        37.71        51.52 
TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GW TCGA-EY-A1GX 
        6.21        23.34        13.97        19.27        11.08         6.48 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A4KR TCGA-EY-A549 TCGA-EY-A72D TCGA-FI-A2D2 
       10.19        14.40        11.38        19.89         5.88        39.95 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ 
        9.07        28.93        45.01         7.76        14.04        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A915 TCGA-QS-A5YQ TCGA-QS-A8F1 
       13.28         9.47         7.00        12.92         4.44 

$`AMP PEAK 19(7Q31.2) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.82        28.27        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-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-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33         1.18        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK 
       19.79        29.39        34.36        34.16         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.49        22.26        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        10.19        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       12.82         2.70         0.13        83.67        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       86.07         8.22        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.20        20.91       117.99       110.37        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-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         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-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-A1CA 
       40.11        65.88        13.28        19.20        16.96        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-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 
       25.12        36.39        11.08         4.77        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.30         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        80.38        46.75        48.76        40.67        44.71 
TCGA-B5-A0JY TCGA-B5-A0JZ TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0K6 
       32.55        28.64        30.51        25.91        27.29        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-A1MW 
       19.50        18.41        17.36        16.57       191.84        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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        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-A0MT 
       48.56        23.47        43.30        43.04        39.32        21.17 
TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       20.28        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        20.02        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
       11.31         6.81        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-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-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-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZQ 
       49.55        63.16        66.48        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-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         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
       14.73         1.58         7.00        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.08        26.37        10.22         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NZ 
        2.33        22.92         1.41        13.22        18.25        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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27         4.11        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R 
        6.67         7.36        16.80        10.92        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       26.96        22.26        16.34        14.53        24.89        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ 
        4.54        53.88        24.36        27.16        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       22.78         6.90        18.84        17.88        17.62        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       16.11        12.43        15.81        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        20.05        45.76        31.04        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX 
       13.84        17.92        14.14        14.70        16.96        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR 
       59.01        28.96        25.02        29.23        41.06         1.74 
TCGA-KJ-A3U4 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        2.43        26.10        18.21        23.24        15.45        23.97 
TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YR 
       12.92        11.24         6.97        18.84        39.95        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE 
                         0.20                          0.07 
  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 
                        16.87                         24.36 
[1] "0.2 - 125.4 (16.9)" "0.1 - 191.8 (24.4)"
[1] "hr=" "3.3"
D19V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 19(7Q31.2) MUTATED                                        51
  AMP PEAK 19(7Q31.2) WILD-TYPE                                     344
                               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                                  34
  AMP PEAK 19(7Q31.2) WILD-TYPE                                78
D19V3, multiclass
                                         clus
vv                                        AMP PEAK 19(7Q31.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          51
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                34
                                         clus
vv                                        AMP PEAK 19(7Q31.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           344
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D19V4, binary
                               cls
clus                              0   1
  AMP PEAK 19(7Q31.2) MUTATED    15  75
  AMP PEAK 19(7Q31.2) WILD-TYPE 126 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(7Q31.2) MUTATED     15   75
  AMP PEAK 19(7Q31.2) WILD-TYPE  126  312
     clus
vv    AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE
  NO                           15                           126
  YES                          75                           312
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 19(7Q31.2) MUTATED    59   3   5   7
  AMP PEAK 19(7Q31.2) WILD-TYPE 304  20  12  28
D19V5, multiclass
    clus
vv   AMP PEAK 19(7Q31.2) MUTATED AMP PEAK 19(7Q31.2) WILD-TYPE
  R0                          59                           304
  R1                           3                            20
  R2                           5                            12
  RX                           7                            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 19(7Q31.2) MUTATED                                  0     3
  AMP PEAK 19(7Q31.2) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 19(7Q31.2) MUTATED                          17
  AMP PEAK 19(7Q31.2) WILD-TYPE                        84
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 19(7Q31.2) MUTATED                                           0    66
  AMP PEAK 19(7Q31.2) WILD-TYPE                                         9   300
D19V6, multiclass
                                           clus
vv                                          AMP PEAK 19(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              66
                                           clus
vv                                          AMP PEAK 19(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            84
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  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"
D19V7, binary
                               cls
clus                              0   1
  AMP PEAK 19(7Q31.2) MUTATED     1  70
  AMP PEAK 19(7Q31.2) WILD-TYPE  13 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 19(7Q31.2) MUTATED      1   70
  AMP PEAK 19(7Q31.2) WILD-TYPE   13  297
                        clus
vv                       AMP PEAK 19(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       AMP PEAK 19(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           297
[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   100  25
  AMP PEAK 20(8P11.22) WILD-TYPE 357  44
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                           125                            401 
  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                            25                             44 
$`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 
       34.16        18.90         1.68         1.64        17.06        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A8CW TCGA-AP-A05A TCGA-AP-A0L8 
       15.62        10.19        14.76         0.13        63.91        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        36.13        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        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-B5-A0JT 
       34.32         0.20         0.20        20.52         0.26        43.13 
TCGA-B5-A0K4 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       17.88         4.11         8.71        32.09        33.50        27.35 
TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-BG-A0M0 
       19.56       102.31        14.70       116.25        33.11        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MQ TCGA-BG-A0YU 
       20.94        34.98        28.27        10.72        39.32        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-BS-A0T9 TCGA-BS-A0TE 
       10.22        10.16        24.13        16.64        46.95         4.80 
TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-D1-A0ZU 
       77.95        67.20        73.25        49.55        63.16        28.67 
TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16R 
        4.44         0.66        36.10        37.32        31.07         0.69 
TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 
       28.08        11.15        13.22         2.07         3.52        41.42 
TCGA-D1-A2G6 TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 
        8.48        24.30        31.10        48.36        17.06        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22T TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       10.92        49.15        66.90        57.60        51.52        19.40 
TCGA-EO-A3B0 TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO 
       17.88        24.89        14.99         4.54         6.90        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 
       17.88        17.62        15.81         6.48        19.33        14.40 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A549 TCGA-FI-A2D4 
       22.82        20.05        29.10        17.92        19.89         7.99 
TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-QS-A744 TCGA-QS-A8F1 
       29.23        14.04        13.28        14.83         4.44 

$`AMP PEAK 20(8P11.22) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54        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-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92        36.33         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N 
       91.04        46.32         5.33         5.16         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3EK 
       10.26        29.39        34.36         1.12         0.76        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ 
       22.49        22.26        20.81        36.99        21.21        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        16.87        16.87        22.32        12.82        20.78 
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-A05J TCGA-AP-A05N TCGA-AP-A05O 
        8.22        57.80        45.53        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       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-A1E1 
       55.89        35.54        46.78        49.15         6.71        10.42 
TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        16.24        21.90         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-A1C8 TCGA-AX-A1C9 
       65.88        13.28        19.20        16.96        13.55        15.25 
TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       12.43        20.05        76.83        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF 
       36.39        11.08        30.12        61.18        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
        0.23         0.56        43.82         1.38         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        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-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        27.29        13.74        17.10 
TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.85        11.01       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-A11U 
       54.44        45.90        43.96        40.50        36.82        16.73 
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-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA 
       14.40        11.70        11.87        15.29        12.79        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 
       34.95        18.61        20.19        35.21        22.06        38.37 
TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0MG TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       36.49        41.52        48.56        23.47        43.30        43.04 
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-A0YV 
       16.34        34.29        52.64        52.83        56.58        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-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A13B TCGA-BK-A13C 
       20.02        20.12        11.31        34.98        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-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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G 
       32.58        15.72        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16V 
       11.51        29.92        33.63        10.65        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.01        26.37        10.22         1.51         1.78        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-A2G7 TCGA-D1-A3DA 
       18.02        15.06         1.05         3.95        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       16.31        39.29        36.62        35.38         9.37        12.39 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
      110.10        23.38         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A2CG 
       16.80        37.71        61.74        61.55        46.26        51.42 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 
       34.39        26.43        35.15        17.19        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE 
       22.26        16.34        14.53         6.21        53.88        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-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 
       18.84        15.09        16.11        12.43        11.08        12.59 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       10.19        18.87        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       11.38        14.14        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88        39.95        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-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 
       45.01         1.74         7.76         2.43        23.74         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        18.21        23.24        15.45        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        12.92 
TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.07        18.28         0.07         0.23 

  AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE 
                          0.13                           0.07 
  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 
                         19.56                          23.97 
[1] "0.1 - 118.0 (19.6)" "0.1 - 191.8 (24.0)"
[1] "hr=" "2.1"
D20V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 20(8P11.22) MUTATED                                        93
  AMP PEAK 20(8P11.22) WILD-TYPE                                     302
                                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                                  26
  AMP PEAK 20(8P11.22) WILD-TYPE                                86
D20V3, multiclass
                                         clus
vv                                        AMP PEAK 20(8P11.22) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           93
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 26
                                         clus
vv                                        AMP PEAK 20(8P11.22) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            302
  MIXED SEROUS AND ENDOMETRIOID                                       15
  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"
D20V4, binary
                                cls
clus                               0   1
  AMP PEAK 20(8P11.22) MUTATED    29  96
  AMP PEAK 20(8P11.22) WILD-TYPE 112 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(8P11.22) MUTATED     29   96
  AMP PEAK 20(8P11.22) WILD-TYPE  112  291
     clus
vv    AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE
  NO                            29                            112
  YES                           96                            291
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(8P11.22) MUTATED    86   4   5  10
  AMP PEAK 20(8P11.22) WILD-TYPE 277  19  12  25
D20V5, multiclass
    clus
vv   AMP PEAK 20(8P11.22) MUTATED AMP PEAK 20(8P11.22) WILD-TYPE
  R0                           86                            277
  R1                            4                             19
  R2                            5                             12
  RX                           10                             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 20(8P11.22) MUTATED                                  0     7
  AMP PEAK 20(8P11.22) WILD-TYPE                                4    13
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 20(8P11.22) MUTATED                          25
  AMP PEAK 20(8P11.22) WILD-TYPE                        76
                                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      83
  AMP PEAK 20(8P11.22) WILD-TYPE   283
D20V6, multiclass
                                           clus
vv                                          AMP PEAK 20(8P11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                7
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            4
  WHITE                                                               83
                                           clus
vv                                          AMP PEAK 20(8P11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 13
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              5
  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"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(8P11.22) MUTATED     2  94
  AMP PEAK 20(8P11.22) WILD-TYPE  12 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(8P11.22) MUTATED      2   94
  AMP PEAK 20(8P11.22) WILD-TYPE   12  273
                        clus
vv                       AMP PEAK 20(8P11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 20(8P11.22) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            273
[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   126  35
  AMP PEAK 21(8P11.21) WILD-TYPE 331  34
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                           161                            365 
  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                            35                             34 
$`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        14.43         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3IA 
        2.40        34.16        18.90         1.68         1.64        20.81 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A8CW 
       20.65        15.62        10.19        14.76        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        21.90        36.13        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        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G1 
       81.37        34.32        64.93         0.20         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K4 
        1.38         0.26         0.39        80.38        43.13        17.88 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
       17.85         4.11         8.71        32.09        33.50        27.35 
TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MW TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD 
       19.56       102.31        14.70        11.87       116.25        33.11 
TCGA-B5-A5OE TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M8 TCGA-BG-A0M9 
       34.95        19.33        20.94        34.98        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MQ TCGA-BG-A0YU TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE 
       10.72        39.32        14.83        15.45         1.81        23.70 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD 
        6.81        35.90         6.21        10.22        24.13        16.64 
TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0V8 
       46.95         4.80        77.95        67.20        73.25        49.55 
TCGA-BS-A0VI TCGA-D1-A0ZU TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A165 TCGA-D1-A168 
       63.16        28.67         4.44        39.48         0.66        36.10 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17R 
       37.32        11.51        31.07         0.69        18.67        11.15 
TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH 
       13.22         2.07         3.52        41.42         8.48         4.11 
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       110.10 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       48.36        17.06        27.32        10.92        49.15        37.71 
TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B0 TCGA-EO-A3B1 
       66.90        51.52        51.42        19.40        17.88        26.96 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ 
       24.89        14.99         4.54         6.90        19.27        17.88 
TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       17.62        15.09        15.81         6.48        19.33        10.19 
TCGA-EY-A214 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A549 TCGA-EY-A72D 
       14.40        22.82        20.05        29.10        19.89         5.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 
       39.95         7.99        96.69         9.07        28.93        29.23 
TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A7D5 
       41.06         7.76        14.04        13.28         9.47        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
       12.92         7.00        14.83         4.44         0.07 

$`AMP PEAK 21(8P11.21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54        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-A0GX TCGA-A5-A0R6 TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        68.65        19.96        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OK 
       29.06        42.35        15.95         7.92        36.33         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O 
       91.04        46.32         5.33         5.16         1.18        10.26 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL 
       29.39        34.36         1.12         0.76        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NF TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       22.26        17.06        36.99        21.21        15.35        15.95 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 
       16.87        22.32        12.82        20.78         2.70        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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG 
       36.89        23.87        12.20        20.91       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-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       60.36        55.89        35.54        46.78        49.15         6.71 
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-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-A1CE TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP 
       20.05        76.83        54.12        67.50        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       11.08        71.24        61.18        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FW 
       17.75        30.74         2.96        31.13         0.23         0.56 
TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82         0.30         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        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-A0K6 
       28.64        28.34        30.51        25.91        27.29        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I 
       17.10        11.01       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-A11U 
       54.44        45.90        43.96        40.50        36.82        16.73 
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-A1MX TCGA-B5-A1MZ TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB 
       14.40        11.70        15.29        12.79        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       62.14        14.27        29.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MG 
       20.19        35.21        22.06        38.37        41.52        48.56 
TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        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-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-A220 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW 
       15.45        14.27         9.57        20.02        20.12        11.31 
TCGA-BK-A0CA TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98        10.16        31.76        24.99        13.18        10.03 
TCGA-BK-A6W4 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ 
        9.86        23.47        85.55        78.21        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-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0WQ 
       81.57        72.72        59.51        62.79        63.58        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-A0ZV TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15W TCGA-D1-A15X 
       23.93        22.55         1.74        21.99        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B 
        1.91         3.68        29.33        32.58        15.72        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        33.63        10.65 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-E6-A1LX TCGA-E6-A2P8 
       27.16        16.31        39.29        36.62        23.38         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        6.67        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GD 
       27.16        22.26        16.34        14.53         6.21        53.88 
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-A1GP TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 
       13.97        18.84        16.11        12.43        11.08        12.59 
TCGA-EY-A215 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       18.87        45.76        31.04        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92        14.14        14.70        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 
       39.88        13.84         8.98        59.01        28.96        25.02 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-KP-A3W4 
       45.01         1.74         2.43        23.74        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        15.45        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.07        18.28         0.23 

  AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE 
                          0.07                           0.23 
  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 
                         19.40                          24.99 
[1] "0.1 - 125.4 (19.4)" "0.2 - 191.8 (25.0)"
[1] "hr=" "2.8"
D21V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 21(8P11.21) MUTATED                                        94
  AMP PEAK 21(8P11.21) WILD-TYPE                                     301
                                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                                  60
  AMP PEAK 21(8P11.21) WILD-TYPE                                52
D21V3, multiclass
                                         clus
vv                                        AMP PEAK 21(8P11.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           94
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 60
                                         clus
vv                                        AMP PEAK 21(8P11.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            301
  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"
D21V4, binary
                                cls
clus                               0   1
  AMP PEAK 21(8P11.21) MUTATED    32 129
  AMP PEAK 21(8P11.21) WILD-TYPE 109 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(8P11.21) MUTATED     32  129
  AMP PEAK 21(8P11.21) WILD-TYPE  109  258
     clus
vv    AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE
  NO                            32                            109
  YES                          129                            258
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(8P11.21) MUTATED   106   4  11  14
  AMP PEAK 21(8P11.21) WILD-TYPE 257  19   6  21
D21V5, multiclass
    clus
vv   AMP PEAK 21(8P11.21) MUTATED AMP PEAK 21(8P11.21) WILD-TYPE
  R0                          106                            257
  R1                            4                             19
  R2                           11                              6
  RX                           14                             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 21(8P11.21) MUTATED                                  1     8
  AMP PEAK 21(8P11.21) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 21(8P11.21) MUTATED                          38
  AMP PEAK 21(8P11.21) WILD-TYPE                        63
                                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     101
  AMP PEAK 21(8P11.21) WILD-TYPE   265
D21V6, multiclass
                                           clus
vv                                          AMP PEAK 21(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                           38
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            4
  WHITE                                                              101
                                           clus
vv                                          AMP PEAK 21(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             63
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              5
  WHITE                                                                265
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(8P11.21) MUTATED     3 118
  AMP PEAK 21(8P11.21) WILD-TYPE  11 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(8P11.21) MUTATED      3  118
  AMP PEAK 21(8P11.21) WILD-TYPE   11  249
                        clus
vv                       AMP PEAK 21(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       AMP PEAK 21(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            249
[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   164  40
  AMP PEAK 22(8Q24.21) WILD-TYPE 293  29
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                           204                            322 
  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                            40                             29 
$`AMP PEAK 22(8Q24.21) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GR 
       41.06        36.69        37.02       105.37        65.75        36.82 
TCGA-A5-A0GW TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 
       23.21        17.59        11.44        36.33         9.60        91.04 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QL 
       28.64         7.33        14.96         1.18         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        2.40        34.16         1.12        18.90         1.68         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.26        17.06        20.81        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AJ-A8CW 
       10.19        14.76        16.87        16.87        20.78         0.13 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LH 
       63.91        45.53        48.79       125.42       117.99        36.36 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E0 TCGA-AP-A3K1 
       97.71        33.40        31.30        46.78        30.90        21.90 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
        0.56        37.78        16.96        13.55        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       76.83        72.56        67.50        11.08         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO 
       71.24        40.80        81.37        34.32         2.96        64.93 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K4 TCGA-B5-A0KB 
        0.30         0.39        80.38        43.13        17.88         4.11 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S 
        8.71        88.34        75.72        32.09        33.50        27.35 
TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW TCGA-B5-A1N2 
       19.56       191.84       102.31        50.89        14.70        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M0 
      116.25        78.81        33.11        34.13        34.95        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        34.98        22.06        36.49        28.27        10.72 
TCGA-BG-A0MT TCGA-BG-A0YU TCGA-BG-A18C TCGA-BG-A221 TCGA-BG-A2AE TCGA-BG-A3PP 
       21.17        14.83        15.45         1.81        23.70         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       35.90         6.21        10.22        10.16        24.13        16.64 
TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TE TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV 
        9.86        46.95         4.80        77.95        67.20        73.25 
TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V 
       63.16        29.95        28.67        22.55         4.44        39.48 
TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N 
        0.66        36.10        37.32        27.42        11.51        31.07 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW 
        0.69        18.67        14.73        11.15        13.22         0.72 
TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DH 
        2.07         3.52        41.42         8.48        44.88         4.11 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
       24.30        35.38         9.37        12.39       110.10        48.36 
TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22T 
       17.06        27.32        10.92        49.15        37.71        66.90 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        51.42        19.40        34.39        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GJ 
       26.96        22.26        24.89        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-A214 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
        6.48        19.33        14.40        22.82        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       27.35        13.84        11.38        17.92        19.89         5.88 
TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV 
        7.99        96.69         9.07        28.93        29.23        41.06 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74         7.76        14.04        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-SL-A6J9 
       18.21        23.97        12.92         7.00        14.83         0.07 

$`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 
       10.29       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 
      112.54        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        14.43        10.26 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       29.39        34.36         0.76        14.66        22.49        36.99 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 
       15.35        15.95        22.32        12.82         2.70        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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LF 
       36.89        23.87        12.20        20.91       110.37         3.39 
TCGA-AP-A0LG TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LN TCGA-AP-A0LP 
       63.16        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-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 
       55.89        35.54        49.15         6.71        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        36.13        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-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP 
       19.20        15.25        20.05        54.12        25.12        36.39 
TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       61.18        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
       31.13         0.23         0.30         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        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        27.29 
TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11F TCGA-B5-A11G 
       13.74        17.10        17.85        11.01       185.79       113.36 
TCGA-B5-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U 
       54.44        45.90        43.96        40.50        36.82        16.73 
TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MX 
       19.50        18.41        17.36        16.57        14.40        11.70 
TCGA-B5-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       11.87        15.29        96.30        62.14        14.27        29.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC 
       41.06        18.61        20.19        35.21        38.37        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-A0YV TCGA-BG-A186 TCGA-BG-A187 
       52.64        52.83        56.58        12.56        13.78        14.73 
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        20.02        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-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TI TCGA-BS-A0TJ TCGA-BS-A0U5 
       23.47        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-A161 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       29.33        32.58        15.72        36.36        37.51        36.79 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-A17U 
       10.22         1.51         1.78        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        3.95         0.26         4.27        16.93        89.33        10.92 
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        16.04         7.36        16.80        61.74 
TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       61.55        46.26        57.60        26.43        35.15        17.19 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       16.34        14.53         6.21        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GT 
       23.34        23.34        22.78        13.97        18.84        16.11 
TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OO 
       12.43        11.08        12.59        10.19        18.87        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       31.04        14.14        14.70        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 
       39.88        39.95        13.84         8.98        59.01        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-PG-A5BC TCGA-PG-A6IB 
       25.02        45.01         2.43        23.74        23.24        15.45 
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        12.92        23.64 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE 
                          0.07                           0.23 
  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 
                        20.715                         24.805 
[1] "0.1 - 191.8 (20.7)" "0.2 - 185.8 (24.8)"
[1] "hr=" "2.4"
D22V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 22(8Q24.21) MUTATED                                       116
  AMP PEAK 22(8Q24.21) WILD-TYPE                                     279
                                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                                  80
  AMP PEAK 22(8Q24.21) WILD-TYPE                                32
D22V3, multiclass
                                         clus
vv                                        AMP PEAK 22(8Q24.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          116
  MIXED SEROUS AND ENDOMETRIOID                                     10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 80
                                         clus
vv                                        AMP PEAK 22(8Q24.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            279
  MIXED SEROUS AND ENDOMETRIOID                                       11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                                cls
clus                               0   1
  AMP PEAK 22(8Q24.21) MUTATED    41 165
  AMP PEAK 22(8Q24.21) WILD-TYPE 100 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(8Q24.21) MUTATED     41  165
  AMP PEAK 22(8Q24.21) WILD-TYPE  100  222
     clus
vv    AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE
  NO                            41                            100
  YES                          165                            222
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(8Q24.21) MUTATED   139   6  10  15
  AMP PEAK 22(8Q24.21) WILD-TYPE 224  17   7  20
D22V5, multiclass
    clus
vv   AMP PEAK 22(8Q24.21) MUTATED AMP PEAK 22(8Q24.21) WILD-TYPE
  R0                          139                            224
  R1                            6                             17
  R2                           10                              7
  RX                           15                             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 22(8Q24.21) MUTATED                                  1     8
  AMP PEAK 22(8Q24.21) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 22(8Q24.21) MUTATED                          50
  AMP PEAK 22(8Q24.21) WILD-TYPE                        51
                                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     132
  AMP PEAK 22(8Q24.21) WILD-TYPE   234
D22V6, multiclass
                                           clus
vv                                          AMP PEAK 22(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                           50
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                              132
                                           clus
vv                                          AMP PEAK 22(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             51
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                234
[1] 5 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     4 150
  AMP PEAK 22(8Q24.21) WILD-TYPE  10 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(8Q24.21) MUTATED      4  150
  AMP PEAK 22(8Q24.21) WILD-TYPE   10  217
                        clus
vv                       AMP PEAK 22(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          150
                        clus
vv                       AMP PEAK 22(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            217
[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   170  40
  AMP PEAK 23(8Q24.21) WILD-TYPE 287  29
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                           210                            316 
  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                            40                             29 
$`AMP PEAK 23(8Q24.21) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GW 
       41.06        36.69        37.02       105.37        65.75        23.21 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-A5-A2K4 
       17.59        11.44        36.33         9.60        91.04        28.64 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        7.33        14.96         1.18         0.39        19.79         2.40 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       34.16         1.12        18.90         1.68         1.64        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A052 
       10.19        14.76        16.87        16.87         0.13        21.99 
TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LF 
       63.91        45.53        48.79       125.42       117.99         3.39 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E0 TCGA-AP-A3K1 
       97.71        33.40        31.30        46.78        30.90        21.90 
TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
        0.56        37.78        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H2 
       12.43        76.83        72.56        67.50        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HK 
       30.12        71.24        40.80        81.37        34.32         2.96 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       64.93         0.20        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K4 
        0.30         0.30         0.39        80.38        43.13        17.88 
TCGA-B5-A11E TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11Q TCGA-B5-A11R 
        8.71        88.34        75.72        45.90        32.09        33.50 
TCGA-B5-A11S TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MW 
       27.35        19.56       191.84       102.31        50.89        14.70 
TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       12.79       116.25        33.11        29.65        34.13        34.95 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0M9 
       19.33        20.94        34.98        22.06        36.49        28.27 
TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MT TCGA-BG-A0YV TCGA-BG-A187 TCGA-BG-A18C 
       10.72        48.56        21.17        12.56        14.73        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-A0TA TCGA-BS-A0TE 
       10.16        24.13        16.64        46.95        23.47         4.80 
TCGA-BS-A0TG TCGA-BS-A0U9 TCGA-BS-A0UV TCGA-BS-A0VI TCGA-D1-A0ZP TCGA-D1-A0ZU 
       77.95        67.20        73.25        63.16        29.95        28.67 
TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A168 
       22.55         4.44        39.48        29.33         0.66        36.10 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A179 
       37.32        11.51        31.07         0.69        18.67        14.73 
TCGA-D1-A17R TCGA-D1-A17U TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 
       11.15        22.92        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       110.10        48.36        17.06        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22T TCGA-EO-A22Y TCGA-EO-A2CG 
       10.92        49.15        37.71        66.90        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       19.40        34.39        27.16        17.88        26.96        22.26 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO 
       24.89        14.99         4.54        23.90         6.90        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 
       17.88        17.62        15.09        15.81         6.48        19.33 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OQ 
       10.19        14.40        18.87        22.82        20.05        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A549 TCGA-EY-A72D 
       27.35        13.84        11.38        17.92        19.89         5.88 
TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV 
        7.99        96.69         9.07        28.93        29.23        41.06 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74         7.76        14.04        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A744 TCGA-SL-A6J9 
       18.21        23.97        12.92         7.00        14.83         0.07 

$`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 
       10.29       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 
      112.54        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        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3EK TCGA-AJ-A3EL 
       10.26        29.39        34.36         0.76        14.66        22.49 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.35        15.95        22.32        12.82        20.78         2.70 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D 
       83.67         5.95        23.31        86.07         8.22        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LE TCGA-AP-A0LG 
       36.89        23.87        12.20        20.91       110.37        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-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E1 TCGA-AP-A1E3 
       55.89        35.54        49.15         6.71        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        36.13        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-A1CE TCGA-AX-A1CJ TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H8 
       19.20        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 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.23         0.56         0.26         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        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-A0K6 
       28.64        28.34        30.51        25.91        27.29        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11F TCGA-B5-A11G 
       17.10        17.85        11.01         4.11       185.79       113.36 
TCGA-B5-A11J TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11W 
       54.44        43.96        40.50        36.82        16.73        19.50 
TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MV TCGA-B5-A1MX TCGA-B5-A1MY 
       18.41        17.36        16.57        14.40        11.70        11.87 
TCGA-B5-A1MZ TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
       15.29        96.30        78.81        62.14        14.27        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0MC TCGA-BG-A0MI 
       18.61        20.19        35.21        38.37        41.52        23.47 
TCGA-BG-A0MK TCGA-BG-A0MO TCGA-BG-A0MQ TCGA-BG-A0MS TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        39.32        30.81        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-A18A TCGA-BG-A18B TCGA-BG-A220 
       56.58        14.83        13.78        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        20.02        20.12        11.31        34.98        31.76 
TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TC TCGA-BS-A0TD 
       24.99        13.18        10.03         9.86        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-A163 TCGA-D1-A167 TCGA-D1-A16B 
       29.88         1.91         3.68        32.58        15.72        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        27.42        29.92        33.63        10.65 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       24.30         2.33         1.41        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
       15.06         1.05         3.95         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       31.10        23.38         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU 
       16.80        61.74        61.55        46.26        57.60        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G7 TCGA-EY-A1GD 
       35.15        17.19        16.34        14.53         6.21        53.88 
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-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2OO 
       18.84        16.11        12.43        11.08        12.59        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       31.04        14.14        14.70        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 
       39.88        39.95        13.84         8.98        59.01        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-PG-A5BC TCGA-PG-A6IB 
       25.02        45.01         2.43        23.74        23.24        15.45 
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        12.92        23.64 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE 
                          0.07                           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 
                         20.73                          25.05 
[1] "0.1 - 191.8 (20.7)" "0.2 - 185.8 (25.0)"
[1] "hr=" "2.3"
D23V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 23(8Q24.21) MUTATED                                       119
  AMP PEAK 23(8Q24.21) WILD-TYPE                                     276
                                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                                  84
  AMP PEAK 23(8Q24.21) WILD-TYPE                                28
D23V3, multiclass
                                         clus
vv                                        AMP PEAK 23(8Q24.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          119
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 84
                                         clus
vv                                        AMP PEAK 23(8Q24.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            276
  MIXED SEROUS AND ENDOMETRIOID                                       12
  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"
D23V4, binary
                                cls
clus                               0   1
  AMP PEAK 23(8Q24.21) MUTATED    42 170
  AMP PEAK 23(8Q24.21) WILD-TYPE  99 217
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(8Q24.21) MUTATED     42  170
  AMP PEAK 23(8Q24.21) WILD-TYPE   99  217
     clus
vv    AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE
  NO                            42                             99
  YES                          170                            217
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(8Q24.21) MUTATED   143   6  13  14
  AMP PEAK 23(8Q24.21) WILD-TYPE 220  17   4  21
D23V5, multiclass
    clus
vv   AMP PEAK 23(8Q24.21) MUTATED AMP PEAK 23(8Q24.21) WILD-TYPE
  R0                          143                            220
  R1                            6                             17
  R2                           13                              4
  RX                           14                             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 23(8Q24.21) MUTATED                                  1     8
  AMP PEAK 23(8Q24.21) WILD-TYPE                                3    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 23(8Q24.21) MUTATED                          46
  AMP PEAK 23(8Q24.21) WILD-TYPE                        55
                                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     140
  AMP PEAK 23(8Q24.21) WILD-TYPE   226
D23V6, multiclass
                                           clus
vv                                          AMP PEAK 23(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                8
  BLACK OR AFRICAN AMERICAN                                           46
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            5
  WHITE                                                              140
                                           clus
vv                                          AMP PEAK 23(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 12
  BLACK OR AFRICAN AMERICAN                                             55
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              4
  WHITE                                                                226
[1] 5 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     5 153
  AMP PEAK 23(8Q24.21) WILD-TYPE   9 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(8Q24.21) MUTATED      5  153
  AMP PEAK 23(8Q24.21) WILD-TYPE    9  214
                        clus
vv                       AMP PEAK 23(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          153
                        clus
vv                       AMP PEAK 23(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            214
[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    49  14
  AMP PEAK 24(9P24.2) WILD-TYPE 408  55
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           63                           463 
  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                           14                            55 
$`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        29.39 
TCGA-AJ-A3EM TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A5FX TCGA-AX-A05Z TCGA-AX-A06B 
       22.26        36.89       125.42        36.13        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         1.38         0.39        80.38        27.29 
TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-BG-A0M6 TCGA-BG-A0YV 
       88.34        75.72        11.87        29.65        22.06        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 
       14.73         0.72        44.88        31.10        17.06        27.32 
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 
       11.08        10.19        20.05        29.10        13.84        11.38 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3VZ 
       96.69        29.23        41.06        45.01         1.74        23.74 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-SL-A6J9 
       23.97        12.92         0.07 

$`AMP PEAK 24(9P24.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 
        7.92        36.33         9.60         8.02        46.32        28.64 
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        14.43        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90         1.68         1.64        14.66        22.49        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       45.53        23.87        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        46.78        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        21.90         0.56        13.58 
TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A060 TCGA-AX-A062 
       19.82        29.69        68.35        72.03        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A06J TCGA-AX-A06L 
       66.58        34.98        12.26        27.39        30.02        60.66 
TCGA-AX-A0IS TCGA-AX-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        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-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39         4.77        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       46.49        26.33        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 
        0.23         0.20         0.56        43.82         0.20         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.26         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-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-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-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11P 
      113.36        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-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-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        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-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        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.16        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-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-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-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-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-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-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.52        41.42         8.48         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       36.62        24.30        35.38         9.37        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        48.36         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        51.52        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        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-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        19.27        18.84        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 
       15.81         6.48        19.33        12.59        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A548 
       22.82        45.76        31.04        27.35        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       39.88        39.95         7.99        13.84         8.98        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-JU-AAVI TCGA-K6-A3WQ 
        9.07        28.93        28.96        25.02         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE 
                         0.07                          0.13 
  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 
                        23.97                         23.31 
[1] "0.1 - 125.4 (24.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.9"
D24V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 24(9P24.2) MUTATED                                        25
  AMP PEAK 24(9P24.2) WILD-TYPE                                     370
                               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                                  36
  AMP PEAK 24(9P24.2) WILD-TYPE                                76
D24V3, multiclass
                                         clus
vv                                        AMP PEAK 24(9P24.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          25
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                36
                                         clus
vv                                        AMP PEAK 24(9P24.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           370
  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"
D24V4, binary
                               cls
clus                              0   1
  AMP PEAK 24(9P24.2) MUTATED    13  51
  AMP PEAK 24(9P24.2) WILD-TYPE 128 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(9P24.2) MUTATED     13   51
  AMP PEAK 24(9P24.2) WILD-TYPE  128  336
     clus
vv    AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE
  NO                           13                           128
  YES                          51                           336
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 24(9P24.2) MUTATED    39   3   3   8
  AMP PEAK 24(9P24.2) WILD-TYPE 324  20  14  27
D24V5, multiclass
    clus
vv   AMP PEAK 24(9P24.2) MUTATED AMP PEAK 24(9P24.2) WILD-TYPE
  R0                          39                           324
  R1                           3                            20
  R2                           3                            14
  RX                           8                            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 24(9P24.2) MUTATED                                  0     1
  AMP PEAK 24(9P24.2) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 24(9P24.2) MUTATED                          19
  AMP PEAK 24(9P24.2) WILD-TYPE                        82
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 24(9P24.2) MUTATED                                           1    38
  AMP PEAK 24(9P24.2) WILD-TYPE                                         8   328
D24V6, multiclass
                                           clus
vv                                          AMP PEAK 24(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              38
                                           clus
vv                                          AMP PEAK 24(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            82
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  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"
D24V7, binary
                               cls
clus                              0   1
  AMP PEAK 24(9P24.2) MUTATED     5  43
  AMP PEAK 24(9P24.2) WILD-TYPE   9 324
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(9P24.2) MUTATED      5   43
  AMP PEAK 24(9P24.2) WILD-TYPE    9  324
                        clus
vv                       AMP PEAK 24(9P24.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          43
                        clus
vv                       AMP PEAK 24(9P24.2) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           324
[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    30   8
  AMP PEAK 25(9Q34.3) WILD-TYPE 427  61
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                           38                           488 
  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                            8                            61 
$`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        29.39         1.64        21.99 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0LH TCGA-AW-A1PO TCGA-AX-A0IU 
       63.91        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        64.93         1.38         0.30        27.29 
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        51.42        23.90        15.09        12.59        10.19 
TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-PG-A7D5 TCGA-PG-A914 
       17.92        41.06        29.23         1.74        23.97        12.92 
TCGA-PG-A915 TCGA-SL-A6J9 
        7.00         0.07 

$`AMP PEAK 25(9Q34.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.82        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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       11.44         9.60         8.02        91.04        46.32        28.64 
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        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
       10.26         0.39        19.79         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76        18.90         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
       83.67         5.95        23.31        86.07         8.22        45.53 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        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        46.78        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        21.90        36.13        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-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 
       30.02        60.66        35.01        37.78        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-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 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        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-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        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-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-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        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-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        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-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-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-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       29.92        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22         0.72        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-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
        9.37        12.39        31.10       110.10        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       10.92        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
       53.88        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-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         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        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       29.10        27.35        13.84        11.38        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.70        16.96         5.88        40.01        39.88        39.95 
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-A3PV TCGA-FI-A3PX TCGA-JU-AAVI 
       28.93        28.96        25.02        41.06        45.01         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        15.45        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE 
                         0.07                          0.13 
  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 
                        20.12                         23.36 
[1] "0.1 - 71.2 (20.1)"  "0.1 - 191.8 (23.4)"
[1] "hr=" "2.1"
D25V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 25(9Q34.3) MUTATED                                        13
  AMP PEAK 25(9Q34.3) WILD-TYPE                                     382
                               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                                91
D25V3, multiclass
                                         clus
vv                                        AMP PEAK 25(9Q34.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          13
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                21
                                         clus
vv                                        AMP PEAK 25(9Q34.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           382
  MIXED SEROUS AND ENDOMETRIOID                                      17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V4, binary
                               cls
clus                              0   1
  AMP PEAK 25(9Q34.3) MUTATED    11  27
  AMP PEAK 25(9Q34.3) WILD-TYPE 130 360
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(9Q34.3) MUTATED     11   27
  AMP PEAK 25(9Q34.3) WILD-TYPE  130  360
     clus
vv    AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE
  NO                           11                           130
  YES                          27                           360
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 25(9Q34.3) MUTATED    26   2   2   1
  AMP PEAK 25(9Q34.3) WILD-TYPE 337  21  15  34
D25V5, multiclass
    clus
vv   AMP PEAK 25(9Q34.3) MUTATED AMP PEAK 25(9Q34.3) WILD-TYPE
  R0                          26                           337
  R1                           2                            21
  R2                           2                            15
  RX                           1                            34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(9Q34.3) MUTATED                                  0     1
  AMP PEAK 25(9Q34.3) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  AMP PEAK 25(9Q34.3) MUTATED                          17
  AMP PEAK 25(9Q34.3) WILD-TYPE                        84
                               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   346
D25V6, multiclass
                                           clus
vv                                          AMP PEAK 25(9Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          17
  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                                                                19
  BLACK OR AFRICAN AMERICAN                                            84
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             9
  WHITE                                                               346
[1] 5 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  25
  AMP PEAK 25(9Q34.3) WILD-TYPE  14 342
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(9Q34.3) MUTATED      0   25
  AMP PEAK 25(9Q34.3) WILD-TYPE   14  342
                        clus
vv                       AMP PEAK 25(9Q34.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       AMP PEAK 25(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           342
[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   118  24
  AMP PEAK 26(10Q22.2) WILD-TYPE 339  45
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                           142                            384 
  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                            24                             45 
$`AMP PEAK 26(10Q22.2) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GJ TCGA-A5-A0GU TCGA-A5-A0GV 
       36.69        37.02       105.37        65.75        28.27        20.81 
TCGA-A5-A0R9 TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A2K2 TCGA-AJ-A23M TCGA-AJ-A23O 
       24.62        36.33         9.60        91.04         1.18        10.26 
TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NH 
       29.39        18.90         1.64        17.06        36.99        10.19 
TCGA-AJ-A3QS TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05P TCGA-AP-A0L8 
       16.87         5.95        63.91        36.89        20.91        48.79 
TCGA-AP-A0LD TCGA-AP-A0LI TCGA-AP-A0LJ TCGA-AP-A0LN TCGA-AP-A0LQ TCGA-AP-A1E3 
      117.99        97.71        31.73        82.52        80.78        27.85 
TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A06D 
       16.24        13.58        19.82        29.69        68.35        12.26 
TCGA-AX-A06J TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1CA TCGA-AX-A1CC 
       30.02        28.54        37.78        13.28        20.28        12.43 
TCGA-AX-A1CJ TCGA-AX-A2H2 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX 
       54.12         4.77        17.75         2.96         0.56        43.82 
TCGA-B5-A0JT TCGA-B5-A0K8 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11I TCGA-B5-A11L 
       43.13        17.85         8.71       185.79        75.72        45.90 
TCGA-B5-A11Q TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MV TCGA-B5-A5OD TCGA-BG-A0LX 
       32.09        33.50        27.35        14.40        34.13        20.19 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0MG TCGA-BG-A0MS TCGA-BG-A0RY 
       20.94        35.21        22.06        48.56        30.81        15.42 
TCGA-BG-A0VT TCGA-BG-A0W2 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A3PP TCGA-BK-A0C9 
       24.39        56.58        14.73        14.01         6.81        35.90 
TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0T9 TCGA-BS-A0TI TCGA-BS-A0U7 TCGA-BS-A0UV 
       10.22        16.64        46.95        61.87        30.74        73.25 
TCGA-BS-A0V7 TCGA-BS-A0V8 TCGA-BS-A0WQ TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZU 
       63.58        49.55        66.48        29.95         8.55        28.67 
TCGA-D1-A102 TCGA-D1-A15V TCGA-D1-A15Z TCGA-D1-A161 TCGA-D1-A165 TCGA-D1-A169 
        4.44        39.48         1.91        29.33         0.66        37.32 
TCGA-D1-A16N TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A17T TCGA-D1-A1NX TCGA-D1-A1O0 
       31.07         0.69        18.67         2.33        18.25         2.07 
TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1M0 
       41.42         4.11        35.38         9.37        12.39        17.06 
TCGA-E6-A2P9 TCGA-EO-A1Y7 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3B1 
        6.67        49.15        51.52        51.42        19.40        26.96 
TCGA-EO-A3KU TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1GC TCGA-EY-A1GH TCGA-EY-A1GO 
       22.26        24.89         6.21         4.54        23.34        19.27 
TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       17.88        15.09        16.11        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 
       12.59        14.40        45.76        31.04        29.10        27.35 
TCGA-EY-A72D TCGA-FI-A2D4 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        5.88         7.99        96.69        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A7D5 
       25.02        45.01         1.74        14.04         9.47        23.97 
TCGA-PG-A915 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZJ 
        7.00        14.83         4.44        18.28 

$`AMP PEAK 26(10Q22.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
       32.78       112.54        87.32        74.10        57.53        60.53 
TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR TCGA-A5-A0GW TCGA-A5-A0GX 
       60.53        46.55        38.37        36.82        23.21        68.65 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       19.96        17.59        19.59        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
        7.92        11.44         8.02        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33        14.96        14.43         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40        34.36        34.16         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        22.26        20.81        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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        23.87 
TCGA-AP-A05O TCGA-AP-A0L9 TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20       125.42       110.37         3.39        63.16        36.36 
TCGA-AP-A0LL TCGA-AP-A0LM TCGA-AP-A0LO TCGA-AP-A0LP TCGA-AP-A0LS TCGA-AP-A0LT 
       83.97        27.12        33.40        61.64        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-A3K1 
       46.78        49.15         6.71        30.90        10.42        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A060 TCGA-AX-A062 
       36.13         0.56        72.03        46.45        35.34        45.99 
TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06B TCGA-AX-A06F TCGA-AX-A06H TCGA-AX-A06L 
       66.58        34.98        53.92        51.09        27.39        60.66 
TCGA-AX-A0IS TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 
       35.01        43.82        40.11        65.88        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CK 
       13.55        15.25        20.05        76.83        72.56        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        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       30.74        31.13        64.93         0.23         0.20         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        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-A0K6 TCGA-B5-A0K7 
       30.51        25.91        27.29        17.88        13.74        17.10 
TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11J TCGA-B5-A11N 
       11.01         4.11       113.36        88.34        54.44        43.96 
TCGA-B5-A11O TCGA-B5-A11P TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W TCGA-B5-A11Y 
       40.50        36.82        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-A1MW 
       17.36        16.57       191.84       102.31        50.89        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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0M0 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 
       34.95        18.61        19.33        34.98        38.37        36.49 
TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK TCGA-BG-A0MO 
       28.27        10.72        41.52        23.47        43.30        43.04 
TCGA-BG-A0MQ TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX 
       39.32        21.17        20.28        26.66        16.34        34.29 
TCGA-BG-A0VZ TCGA-BG-A0W1 TCGA-BG-A0YU TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18B 
       52.64        52.83        14.83        12.56        13.78        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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       20.12        11.31        34.98         6.21        10.16        31.76 
TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0TA 
       24.99        24.13        13.18        10.03         9.86        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-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-A0V4 TCGA-BS-A0V6 TCGA-BS-A0VI TCGA-D1-A0ZN TCGA-D1-A0ZO 
       72.72        59.51        62.79        63.16        16.83        19.79 
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-A160 TCGA-D1-A163 TCGA-D1-A167 TCGA-D1-A168 
       30.08        29.88         3.68        32.58        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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       33.63        10.65         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17U 
       10.22         1.51         1.78        11.15        24.30        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22         0.72        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95         3.52         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       39.29        36.62        24.30        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
       48.36         2.37        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       57.60        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       17.88        16.34        14.53        14.99        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A212 TCGA-EY-A215 
       18.84        17.62        12.43        15.81        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       22.82        20.05        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        14.70        16.96        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV 
       39.95        13.84         8.98        28.96        29.23        41.06 
TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
        7.76         2.43        23.74        13.28        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        15.45        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-SJ-A6ZI TCGA-SL-A6J9 TCGA-SL-A6JA 
       39.95        12.92        23.64        14.07         0.07         0.23 

  AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE 
                          0.56                           0.07 
  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 
                         22.80                          23.36 
[1] "0.6 - 185.8 (22.8)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.5"
D26V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 26(10Q22.2) MUTATED                                        96
  AMP PEAK 26(10Q22.2) WILD-TYPE                                     299
                                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                                  44
  AMP PEAK 26(10Q22.2) WILD-TYPE                                68
D26V3, multiclass
                                         clus
vv                                        AMP PEAK 26(10Q22.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           96
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 26(10Q22.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            299
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V4, binary
                                cls
clus                               0   1
  AMP PEAK 26(10Q22.2) MUTATED    34 109
  AMP PEAK 26(10Q22.2) WILD-TYPE 107 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(10Q22.2) MUTATED     34  109
  AMP PEAK 26(10Q22.2) WILD-TYPE  107  278
     clus
vv    AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE
  NO                            34                            107
  YES                          109                            278
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(10Q22.2) MUTATED   103   7   7   7
  AMP PEAK 26(10Q22.2) WILD-TYPE 260  16  10  28
D26V5, multiclass
    clus
vv   AMP PEAK 26(10Q22.2) MUTATED AMP PEAK 26(10Q22.2) WILD-TYPE
  R0                          103                            260
  R1                            7                             16
  R2                            7                             10
  RX                            7                             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 26(10Q22.2) MUTATED                                  2     5
  AMP PEAK 26(10Q22.2) WILD-TYPE                                2    15
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 26(10Q22.2) MUTATED                          28
  AMP PEAK 26(10Q22.2) WILD-TYPE                        73
                                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      98
  AMP PEAK 26(10Q22.2) WILD-TYPE   268
D26V6, multiclass
                                           clus
vv                                          AMP PEAK 26(10Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     2
  ASIAN                                                                5
  BLACK OR AFRICAN AMERICAN                                           28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            4
  WHITE                                                               98
                                           clus
vv                                          AMP PEAK 26(10Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       2
  ASIAN                                                                 15
  BLACK OR AFRICAN AMERICAN                                             73
  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"
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(10Q22.2) MUTATED     3 102
  AMP PEAK 26(10Q22.2) WILD-TYPE  11 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(10Q22.2) MUTATED      3  102
  AMP PEAK 26(10Q22.2) WILD-TYPE   11  265
                        clus
vv                       AMP PEAK 26(10Q22.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       AMP PEAK 26(10Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            265
[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    37  13
  AMP PEAK 27(11P11.2) WILD-TYPE 420  56
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            50                            476 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                            13                             56 
$`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        14.43        22.26        20.81        16.87         5.95 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A0IU TCGA-AX-A0IW 
       45.53        48.79        46.78        36.13        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         1.38        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        29.65        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        14.73 
TCGA-DI-A1NN TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EY-A1GM TCGA-EY-A210 
       35.38       110.10        37.71        51.42         6.90        12.59 
TCGA-EY-A212 TCGA-EY-A72D TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       10.19         5.88        45.01         1.74         7.76        14.04 
TCGA-KP-A3W3 TCGA-PG-A915 
       26.10         7.00 

$`AMP PEAK 27(11P11.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        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-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        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-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP 
       91.04        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        1.18        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
       83.67        21.99        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       57.80        36.89        23.87        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-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-A3K1 TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        21.90         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-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.01        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-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        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       61.18        81.37        34.32        46.49        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        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-A0K3 TCGA-B5-A0K6 TCGA-B5-A0K7 
       28.34        30.51        25.91        27.29        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-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-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 
       34.13        18.61        20.19        19.33        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       22.06        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-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        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-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-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-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-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-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-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-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        17.88        26.96        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        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-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-A214 
       12.43        15.81        11.08         6.48        19.33        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.70        16.96        40.01        41.06        39.88        39.95 
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-KJ-A3U4 
       28.93        28.96        25.02        29.23        41.06         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       23.74        13.28         9.47        18.21        23.24        15.45 
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 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                          1.38                           0.07 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                        110.10                         191.84 
  AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE 
                        20.085                         23.555 
[1] "1.4 - 110.1 (20.1)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.5"
D27V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 27(11P11.2) MUTATED                                        16
  AMP PEAK 27(11P11.2) WILD-TYPE                                     379
                                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                                  30
  AMP PEAK 27(11P11.2) WILD-TYPE                                82
D27V3, multiclass
                                         clus
vv                                        AMP PEAK 27(11P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           16
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 30
                                         clus
vv                                        AMP PEAK 27(11P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            379
  MIXED SEROUS AND ENDOMETRIOID                                       17
  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"
D27V4, binary
                                cls
clus                               0   1
  AMP PEAK 27(11P11.2) MUTATED    12  38
  AMP PEAK 27(11P11.2) WILD-TYPE 129 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(11P11.2) MUTATED     12   38
  AMP PEAK 27(11P11.2) WILD-TYPE  129  349
     clus
vv    AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE
  NO                            12                            129
  YES                           38                            349
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(11P11.2) MUTATED    34   1   2   5
  AMP PEAK 27(11P11.2) WILD-TYPE 329  22  15  30
D27V5, multiclass
    clus
vv   AMP PEAK 27(11P11.2) MUTATED AMP PEAK 27(11P11.2) WILD-TYPE
  R0                           34                            329
  R1                            1                             22
  R2                            2                             15
  RX                            5                             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 27(11P11.2) MUTATED                                  0     1
  AMP PEAK 27(11P11.2) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 27(11P11.2) MUTATED                          13
  AMP PEAK 27(11P11.2) WILD-TYPE                        88
                                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      32
  AMP PEAK 27(11P11.2) WILD-TYPE   334
D27V6, multiclass
                                           clus
vv                                          AMP PEAK 27(11P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           13
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               32
                                           clus
vv                                          AMP PEAK 27(11P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             88
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                334
[1] 5 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  32
  AMP PEAK 27(11P11.2) WILD-TYPE  12 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(11P11.2) MUTATED      2   32
  AMP PEAK 27(11P11.2) WILD-TYPE   12  335
                        clus
vv                       AMP PEAK 27(11P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           32
                        clus
vv                       AMP PEAK 27(11P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            335
[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    54  16
  AMP PEAK 28(11Q13.2) WILD-TYPE 403  53
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            70                            456 
  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                            16                             53 
$`AMP PEAK 28(11Q13.2) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23M 
       36.69        65.75        11.44        36.33         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A05A TCGA-AP-A05J 
       14.43         0.39        20.81        10.19        63.91        36.89 
TCGA-AP-A0L8 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C5 TCGA-AX-A1C9 
       48.79        36.13        53.92        37.78        19.20        15.25 
TCGA-AX-A1CA TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A2HK 
       20.28         4.77        30.12        71.24        19.36         2.96 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-B5-A0JN TCGA-B5-A0JT 
       43.82        20.52         1.38         0.30        80.38        43.13 
TCGA-B5-A0JX TCGA-B5-A0K4 TCGA-B5-A11Q TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FB 
       44.71        17.88        32.09        50.89        12.79        78.81 
TCGA-B5-A3S1 TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0VT TCGA-BG-A18C 
       29.65        20.94        36.49        41.52        24.39        15.45 
TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A169 TCGA-D1-A16I 
       24.13        16.64        67.20        29.95        37.32        11.51 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1O0 TCGA-DI-A1NN TCGA-DI-A2QU 
       18.67         3.95        28.08         2.07        35.38        31.10 
TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A210 
       27.32        49.15        16.34         4.54        23.90        12.59 
TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A3PX 
       10.19        29.10         5.88        41.06         9.07        45.01 
TCGA-K6-A3WQ TCGA-KP-A3W3 TCGA-PG-A914 TCGA-SL-A6J9 
       14.04        26.10        12.92         0.07 

$`AMP PEAK 28(11Q13.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        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-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-A3LP TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        5.16        14.96        10.26        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
       34.36        34.16         1.12         0.76        18.90         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        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-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        23.87        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        46.78        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        21.90 
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-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-A1C7 TCGA-AX-A1C8 
       43.82        40.11        65.88        13.28        16.96        13.55 
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-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       25.12        36.39        11.08        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G4 
       64.93         0.23         0.20         0.56         0.20         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.26         1.18        18.35        14.47         0.39        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-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       30.51        25.91        27.29        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-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-A3F9 TCGA-B5-A3FA TCGA-B5-A3FC 
       11.70        11.87        15.29       116.25        96.30        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       33.11        14.27        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 
       20.19        19.33        35.21        34.98        22.06        38.37 
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-A0VV 
       39.32        30.81        21.17        20.28        15.42        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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 
        6.81        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-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-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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J 
       36.10        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       31.07        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-D1-A3JP 
        8.48        44.88         0.26         4.27         4.11        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ 
       24.30         9.37        12.39       110.10        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        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       57.60        51.52        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        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-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 
       12.43        15.81        11.08         6.48        19.33        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96        40.01        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
        8.98        96.69        59.01        28.93        28.96        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       29.23        41.06         1.74         7.76         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28         9.47        18.21        23.24        15.45        23.97 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        14.07        18.28         0.23 

  AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE 
                          0.07                           0.13 
  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 
                        24.015                         23.325 
[1] "0.1 - 80.4 (24.0)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "2.2"
D28V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 28(11Q13.2) MUTATED                                        33
  AMP PEAK 28(11Q13.2) WILD-TYPE                                     362
                                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                                  34
  AMP PEAK 28(11Q13.2) WILD-TYPE                                78
D28V3, multiclass
                                         clus
vv                                        AMP PEAK 28(11Q13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           33
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 34
                                         clus
vv                                        AMP PEAK 28(11Q13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            362
  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"
D28V4, binary
                                cls
clus                               0   1
  AMP PEAK 28(11Q13.2) MUTATED    16  54
  AMP PEAK 28(11Q13.2) WILD-TYPE 125 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(11Q13.2) MUTATED     16   54
  AMP PEAK 28(11Q13.2) WILD-TYPE  125  333
     clus
vv    AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE
  NO                            16                            125
  YES                           54                            333
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 28(11Q13.2) MUTATED    41   2   4   7
  AMP PEAK 28(11Q13.2) WILD-TYPE 322  21  13  28
D28V5, multiclass
    clus
vv   AMP PEAK 28(11Q13.2) MUTATED AMP PEAK 28(11Q13.2) WILD-TYPE
  R0                           41                            322
  R1                            2                             21
  R2                            4                             13
  RX                            7                             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 28(11Q13.2) MUTATED                                  0     1
  AMP PEAK 28(11Q13.2) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 28(11Q13.2) MUTATED                          17
  AMP PEAK 28(11Q13.2) WILD-TYPE                        84
                                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      48
  AMP PEAK 28(11Q13.2) WILD-TYPE   318
D28V6, multiclass
                                           clus
vv                                          AMP PEAK 28(11Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               48
                                           clus
vv                                          AMP PEAK 28(11Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             84
  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"
D28V7, binary
                                cls
clus                               0   1
  AMP PEAK 28(11Q13.2) MUTATED     1  49
  AMP PEAK 28(11Q13.2) WILD-TYPE  13 318
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 28(11Q13.2) MUTATED      1   49
  AMP PEAK 28(11Q13.2) WILD-TYPE   13  318
                        clus
vv                       AMP PEAK 28(11Q13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           49
                        clus
vv                       AMP PEAK 28(11Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            318
[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    38  18
  AMP PEAK 29(11Q14.1) WILD-TYPE 419  51
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            56                            470 
  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                            18                             51 
$`AMP PEAK 29(11Q14.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LO TCGA-AJ-A23N 
       36.69        37.02        65.75        36.33         7.33        14.43 
TCGA-AJ-A3BF TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A0L8 TCGA-AP-A5FX 
        1.12        20.81        10.19        16.87        48.79        36.13 
TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2HK 
       37.78        20.28        12.43         4.77        30.12         2.96 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0JX 
       20.52         1.38         0.39        80.38        43.13        44.71 
TCGA-B5-A0K4 TCGA-B5-A11Q TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1N2 TCGA-B5-A3FD 
       17.88        32.09       102.31        50.89        12.79        33.11 
TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MC TCGA-BG-A0VT TCGA-BG-A18C TCGA-BG-A3PP 
       20.94        36.49        41.52        24.39        15.45         6.81 
TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A16V TCGA-D1-A1NX TCGA-D1-A1O0 
       16.64        67.20        11.51         3.95        18.25         2.07 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A1Y5 TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A212 
       35.38        12.39        10.92        22.26        23.90        10.19 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2EY TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-PG-A914 
       29.10        11.38        28.93        45.01        14.04        12.92 
TCGA-PG-A915 TCGA-QS-A8F1 
        7.00         4.44 

$`AMP PEAK 29(11Q14.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-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-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16        14.96         1.18        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36        34.16         0.76        18.90 
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        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       14.76        16.87        22.32        12.82        20.78         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-A05J TCGA-AP-A05N 
        8.22        63.91        57.80        45.53        36.89        23.87 
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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 
       46.78        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        21.90         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-A1CE 
       13.28        19.20        16.96        13.55        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-A1CR TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       11.08        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        48.76        40.67        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        27.29        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-A11R TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11V TCGA-B5-A11W 
       36.82        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-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB 
       11.70        11.87        15.29       116.25        96.30        78.81 
TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       18.61        20.19        19.33        35.21        34.98        22.06 
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-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        20.02        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-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-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-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-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69        18.67         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22         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-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        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-A1Y7 
        6.67        27.32        16.04         7.36        16.80        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       51.52        51.42        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        27.16        17.88        26.96        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        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-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         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        20.05        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        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
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-H5-A2HR TCGA-JU-AAVI 
       28.96        25.02        29.23        41.06         1.74         7.76 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        2.43        23.74        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        15.45        23.97        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE 
                          0.39                           0.07 
  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 
                        20.400                         23.555 
[1] "0.4 - 102.3 (20.4)" "0.1 - 191.8 (23.6)"
[1] "hr=" "3.7"
D29V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 29(11Q14.1) MUTATED                                        21
  AMP PEAK 29(11Q14.1) WILD-TYPE                                     374
                                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                                  34
  AMP PEAK 29(11Q14.1) WILD-TYPE                                78
D29V3, multiclass
                                         clus
vv                                        AMP PEAK 29(11Q14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           21
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 34
                                         clus
vv                                        AMP PEAK 29(11Q14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            374
  MIXED SEROUS AND ENDOMETRIOID                                       20
  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"
D29V4, binary
                                cls
clus                               0   1
  AMP PEAK 29(11Q14.1) MUTATED    10  46
  AMP PEAK 29(11Q14.1) WILD-TYPE 131 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(11Q14.1) MUTATED     10   46
  AMP PEAK 29(11Q14.1) WILD-TYPE  131  341
     clus
vv    AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE
  NO                            10                            131
  YES                           46                            341
[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 330  22  14  30
D29V5, multiclass
    clus
vv   AMP PEAK 29(11Q14.1) MUTATED AMP PEAK 29(11Q14.1) WILD-TYPE
  R0                           33                            330
  R1                            1                             22
  R2                            3                             14
  RX                            5                             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 29(11Q14.1) MUTATED                                  1     0
  AMP PEAK 29(11Q14.1) WILD-TYPE                                3    20
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 29(11Q14.1) MUTATED                          16
  AMP PEAK 29(11Q14.1) WILD-TYPE                        85
                                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   331
D29V6, multiclass
                                           clus
vv                                          AMP PEAK 29(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           16
  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                                                                 20
  BLACK OR AFRICAN AMERICAN                                             85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                331
[1] 5 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  38
  AMP PEAK 29(11Q14.1) WILD-TYPE  13 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 29(11Q14.1) MUTATED      1   38
  AMP PEAK 29(11Q14.1) WILD-TYPE   13  329
                        clus
vv                       AMP PEAK 29(11Q14.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           38
                        clus
vv                       AMP PEAK 29(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            329
[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    79  12
  AMP PEAK 30(12P12.1) WILD-TYPE 378  57
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            91                            435 
  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                            12                             57 
$`AMP PEAK 30(12P12.1) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GE TCGA-A5-A0R7 TCGA-A5-A1OG 
       41.06        36.69       149.56       105.37        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3IA 
       36.33        46.32         1.18        34.16         1.12        20.81 
TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A1DO TCGA-AP-A1DQ 
       10.19        16.87        20.91       125.42        31.30        46.78 
TCGA-AP-A1E4 TCGA-AX-A05W TCGA-AX-A0IW TCGA-AX-A0J1 TCGA-AX-A1CA TCGA-AX-A1CR 
       16.24        68.35        37.78        65.88        20.28        11.08 
TCGA-AX-A2H2 TCGA-AX-A2HA TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3G3 TCGA-AX-A3GI 
        4.77        81.37        19.36         2.96         1.38         0.39 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11R TCGA-B5-A11V TCGA-B5-A11W 
       80.38        27.29        17.85        33.50        19.56        19.50 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0M2 
       11.87        12.79        29.65        41.06        34.13        20.94 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MG TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A2AE 
       22.06        36.49        48.56        52.83        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A13B TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 
        6.81        10.16        31.76         4.80        61.87        67.20 
TCGA-BS-A0V7 TCGA-D1-A168 TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A17K TCGA-D1-A17U 
       63.58        36.10        11.51        33.63        28.08        22.92 
TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1C3 TCGA-DI-A1NN 
        2.07        41.42         4.11        16.93        24.30        35.38 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A3AV 
      110.10        48.36        27.32        10.92        51.42        35.15 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A1H0 
       27.16        26.96         4.54        19.27        15.09        19.33 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2D6 
       12.59        14.40        27.35         5.88        39.95         8.98 
TCGA-FI-A2EY TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-PG-A914 
       28.93        45.01         7.76        14.04        23.74        12.92 
TCGA-PG-A915 
        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 
       10.29       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 
      112.54        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        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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        17.06        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         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        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        48.79       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-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        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05Y 
       36.13         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-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C7 
       28.54        43.82        40.11        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-A2H5 
       54.12        67.50        25.12        36.39        30.12        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        61.18        34.32        46.49        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         0.30         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        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-A11P TCGA-B5-A11Q 
       54.44        45.90        43.96        40.50        36.82        32.09 
TCGA-B5-A11S TCGA-B5-A11U TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       27.35        16.73        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-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
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-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MI TCGA-BG-A0MK 
       38.37        28.27        10.72        41.52        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-A0W2 
       24.39        26.66        16.34        34.29        52.64        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-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98         6.21        10.22        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       85.55        78.21        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-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-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-A16Q TCGA-D1-A16R 
       36.79        27.42        29.92        31.07        10.65         0.69 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       18.67         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-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-A1NS TCGA-D1-A1NU 
        1.78        11.15        24.30         2.33         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52         8.48        44.88         0.26         4.27 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-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-A1Y7 TCGA-EO-A1Y8 
        6.67        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU 
       19.40        34.39        26.43        17.19        17.88        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
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-A1GR TCGA-EY-A1GT 
       13.97         6.90        18.84        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A212 TCGA-EY-A215 
       12.43        15.81        11.08         6.48        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        29.10        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       11.38        17.92        14.14        19.89        14.70        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU 
       40.01        41.06        39.88         7.99        13.84        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        29.23        41.06 
TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        1.74         2.43        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       23.24        15.45        23.97        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE 
                          0.39                           0.07 
  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 
                         23.70                          23.34 
[1] "0.4 - 149.6 (23.7)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1"  
D30V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 30(12P12.1) MUTATED                                        44
  AMP PEAK 30(12P12.1) WILD-TYPE                                     351
                                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                                  44
  AMP PEAK 30(12P12.1) WILD-TYPE                                68
D30V3, multiclass
                                         clus
vv                                        AMP PEAK 30(12P12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           44
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 30(12P12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            351
  MIXED SEROUS AND ENDOMETRIOID                                       17
  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"
D30V4, binary
                                cls
clus                               0   1
  AMP PEAK 30(12P12.1) MUTATED    20  72
  AMP PEAK 30(12P12.1) WILD-TYPE 121 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(12P12.1) MUTATED     20   72
  AMP PEAK 30(12P12.1) WILD-TYPE  121  315
     clus
vv    AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE
  NO                            20                            121
  YES                           72                            315
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 30(12P12.1) MUTATED    65   2   3   4
  AMP PEAK 30(12P12.1) WILD-TYPE 298  21  14  31
D30V5, multiclass
    clus
vv   AMP PEAK 30(12P12.1) MUTATED AMP PEAK 30(12P12.1) WILD-TYPE
  R0                           65                            298
  R1                            2                             21
  R2                            3                             14
  RX                            4                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 30(12P12.1) MUTATED                                  0     6
  AMP PEAK 30(12P12.1) WILD-TYPE                                4    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 30(12P12.1) MUTATED                          24
  AMP PEAK 30(12P12.1) WILD-TYPE                        77
                                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      56
  AMP PEAK 30(12P12.1) WILD-TYPE   310
D30V6, multiclass
                                           clus
vv                                          AMP PEAK 30(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           24
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               56
                                           clus
vv                                          AMP PEAK 30(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             77
  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"
D30V7, binary
                                cls
clus                               0   1
  AMP PEAK 30(12P12.1) MUTATED     0  68
  AMP PEAK 30(12P12.1) WILD-TYPE  14 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 30(12P12.1) MUTATED      0   68
  AMP PEAK 30(12P12.1) WILD-TYPE   14  299
                        clus
vv                       AMP PEAK 30(12P12.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       AMP PEAK 30(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 14
  NOT HISPANIC OR LATINO                            299
[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    74  10
  AMP PEAK 31(12Q13.11) WILD-TYPE 383  59
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             84                             442 
  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                             10                              59 
$`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        34.16         1.12        22.26        16.87 
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        81.37         2.96         0.20         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A11R TCGA-B5-A11V 
        0.30         0.30         0.39        27.29        33.50        19.56 
TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MG 
       12.79        29.65        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-D1-A3JP TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       44.88        16.93        24.30        35.38        12.39       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AV TCGA-EY-A1GJ 
       48.36        27.32        49.15        51.42        35.15        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A214 
        6.90        19.27        17.62        19.33        12.59        14.40 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EY 
       27.35        11.38        39.95         8.98        59.01        28.93 
TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-PG-A7D5 TCGA-PG-A914 TCGA-SL-A6J9 
       45.01        14.04        23.74        23.97        12.92         0.07 

$`AMP PEAK 31(12Q13.11) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        36.69        10.29       106.88        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54        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-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-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.49        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
       21.99        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0LD 
       45.53        36.89        23.87        12.20        48.79       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-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 
       46.78        49.15         6.71        30.90        10.42        27.85 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       21.90        36.13         0.56        13.58        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-A0IZ TCGA-AX-A0J0 TCGA-AX-A1C4 TCGA-AX-A1C5 
       35.01        28.54        43.82        40.11        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-A2H5 
       72.56        54.12        67.50        25.12        36.39        71.24 
TCGA-AX-A2H7 TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       40.80        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82        20.52         0.26         1.18        18.35        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-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-A11S 
       45.90        43.96        40.50        36.82        32.09        27.35 
TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       16.73        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-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-A3FH TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        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 
       20.02        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-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-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-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-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-A16Q 
       36.79        27.42        11.51        29.92        31.07        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-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-A2G6 TCGA-D1-A3DA 
       15.06         1.05         3.95         3.52         8.48         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       39.29        36.62         9.37        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        16.04         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        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.52        19.40        34.39        26.43        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.34        23.34        22.78        13.97        18.84        17.88 
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        11.08         6.48 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       10.19        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       29.10        13.84        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       13.84        96.69         9.07        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.06         1.74         7.76         2.43        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
       26.10        18.21        23.24        15.45         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE 
                           0.07                            0.13 
  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 
                         23.935                          23.225 
[1] "0.1 - 149.6 (23.9)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.2"
D31V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 31(12Q13.11) MUTATED                                        39
  AMP PEAK 31(12Q13.11) WILD-TYPE                                     356
                                 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                                  41
  AMP PEAK 31(12Q13.11) WILD-TYPE                                71
D31V3, multiclass
                                         clus
vv                                        AMP PEAK 31(12Q13.11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            39
  MIXED SEROUS AND ENDOMETRIOID                                       4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  41
                                         clus
vv                                        AMP PEAK 31(12Q13.11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             356
  MIXED SEROUS AND ENDOMETRIOID                                        17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V4, binary
                                 cls
clus                                0   1
  AMP PEAK 31(12Q13.11) MUTATED    16  68
  AMP PEAK 31(12Q13.11) WILD-TYPE 125 319
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(12Q13.11) MUTATED     16   68
  AMP PEAK 31(12Q13.11) WILD-TYPE  125  319
     clus
vv    AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE
  NO                             16                             125
  YES                            68                             319
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 31(12Q13.11) MUTATED    57   2   5   7
  AMP PEAK 31(12Q13.11) WILD-TYPE 306  21  12  28
D31V5, multiclass
    clus
vv   AMP PEAK 31(12Q13.11) MUTATED AMP PEAK 31(12Q13.11) WILD-TYPE
  R0                            57                             306
  R1                             2                              21
  R2                             5                              12
  RX                             7                              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 31(12Q13.11) MUTATED                                  1     6
  AMP PEAK 31(12Q13.11) WILD-TYPE                                3    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 31(12Q13.11) MUTATED                          23
  AMP PEAK 31(12Q13.11) WILD-TYPE                        78
                                 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      49
  AMP PEAK 31(12Q13.11) WILD-TYPE   317
D31V6, multiclass
                                           clus
vv                                          AMP PEAK 31(12Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                49
                                           clus
vv                                          AMP PEAK 31(12Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              78
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  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"
D31V7, binary
                                 cls
clus                                0   1
  AMP PEAK 31(12Q13.11) MUTATED     1  62
  AMP PEAK 31(12Q13.11) WILD-TYPE  13 305
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 31(12Q13.11) MUTATED      1   62
  AMP PEAK 31(12Q13.11) WILD-TYPE   13  305
                        clus
vv                       AMP PEAK 31(12Q13.11) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            62
                        clus
vv                       AMP PEAK 31(12Q13.11) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             305
[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    82  14
  AMP PEAK 32(12Q13.2) WILD-TYPE 375  55
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            96                            430 
  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                            14                             55 
$`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        34.16         1.12 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A05P 
       22.26        17.06        10.19        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        81.37        19.36         0.56 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11R TCGA-B5-A11V 
       43.82        20.52        27.29        17.85        33.50        19.56 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0M2 TCGA-BG-A0M8 TCGA-BG-A0MG 
       29.65        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-D1-A3JP TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
        4.11        16.93        24.30        35.38        12.39       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AV 
       48.36        27.32        49.15        37.71        51.42        35.15 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1H0 TCGA-EY-A210 
        4.54        23.90        19.27        17.62        19.33        12.59 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A72D TCGA-FI-A2CX 
       14.40        20.05        27.35        13.84         5.88        40.01 
TCGA-FI-A2D2 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       39.95         8.98        59.01        29.23        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-PG-A7D5 TCGA-SL-A6J9 
        7.76        14.04         2.43        23.74        23.97         0.07 

$`AMP PEAK 32(12Q13.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        36.69        10.29       106.88        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54        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-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-A2K2 
       15.95         7.92        36.33         9.60         8.02        91.04 
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        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79        29.39         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA 
       18.90         1.68         1.64        14.66        22.49        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        63.91        57.80        36.89        23.87        12.20 
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-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-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        49.15         6.71        30.90        10.42 
TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        21.90        36.13         0.56        13.58        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-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-A1C4 
       60.66        35.01        28.54        43.82        40.11        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-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        71.24        40.80        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 
       31.13        64.93         0.23         0.20         0.20         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-A11P TCGA-B5-A11Q TCGA-B5-A11S 
       45.90        43.96        40.50        36.82        32.09        27.35 
TCGA-B5-A11U TCGA-B5-A11W TCGA-B5-A11Y TCGA-B5-A11Z TCGA-B5-A121 TCGA-B5-A1MR 
       16.73        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-A3FH TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       33.11        14.27        34.95        18.61        20.19        19.33 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        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 
       20.02        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-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-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        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-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16Q 
       36.79        27.42        11.51        29.92        31.07        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-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-A2G6 TCGA-D1-A2G7 
       15.06         1.05         3.95         3.52         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26         4.27        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       39.29        36.62         9.37        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        16.04         7.36        16.80        10.92 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       19.40        34.39        26.43        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       26.96        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       22.78        13.97         6.90        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A212 
       16.11        12.43        15.81        11.08         6.48        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A4KR 
       18.87        22.82        45.76        31.04        29.10        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       17.92        14.14        19.89        14.70        16.96        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY 
       39.88         7.99        13.84        96.69         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       28.96        25.02        41.06        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       18.21        23.24        15.45        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE 
                          0.07                           0.13 
  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 
                        22.125                         23.360 
[1] "0.1 - 149.6 (22.1)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.1"
D32V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 32(12Q13.2) MUTATED                                        49
  AMP PEAK 32(12Q13.2) WILD-TYPE                                     346
                                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                                  44
  AMP PEAK 32(12Q13.2) WILD-TYPE                                68
D32V3, multiclass
                                         clus
vv                                        AMP PEAK 32(12Q13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           49
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 32(12Q13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            346
  MIXED SEROUS AND ENDOMETRIOID                                       17
  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"
D32V4, binary
                                cls
clus                               0   1
  AMP PEAK 32(12Q13.2) MUTATED    18  79
  AMP PEAK 32(12Q13.2) WILD-TYPE 123 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(12Q13.2) MUTATED     18   79
  AMP PEAK 32(12Q13.2) WILD-TYPE  123  308
     clus
vv    AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE
  NO                            18                            123
  YES                           79                            308
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 32(12Q13.2) MUTATED    69   3   7   5
  AMP PEAK 32(12Q13.2) WILD-TYPE 294  20  10  30
D32V5, multiclass
    clus
vv   AMP PEAK 32(12Q13.2) MUTATED AMP PEAK 32(12Q13.2) WILD-TYPE
  R0                           69                            294
  R1                            3                             20
  R2                            7                             10
  RX                            5                             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 32(12Q13.2) MUTATED                                  1     6
  AMP PEAK 32(12Q13.2) WILD-TYPE                                3    14
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 32(12Q13.2) MUTATED                          25
  AMP PEAK 32(12Q13.2) WILD-TYPE                        76
                                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      59
  AMP PEAK 32(12Q13.2) WILD-TYPE   307
D32V6, multiclass
                                           clus
vv                                          AMP PEAK 32(12Q13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                6
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               59
                                           clus
vv                                          AMP PEAK 32(12Q13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 14
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                307
[1] 5 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  74
  AMP PEAK 32(12Q13.2) WILD-TYPE  12 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 32(12Q13.2) MUTATED      2   74
  AMP PEAK 32(12Q13.2) WILD-TYPE   12  293
                        clus
vv                       AMP PEAK 32(12Q13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       AMP PEAK 32(12Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            293
[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   9
  AMP PEAK 33(13Q34) WILD-TYPE 409  60
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                          57                          469 
  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                           9                           60 
$`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        14.43 
TCGA-AJ-A3IA TCGA-AJ-A3QS TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A1DV 
       20.81        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 
       64.93         1.38        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 
       29.65        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       110.10        48.36        10.92        51.52        51.42 
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-KP-A3VZ 
       27.35        11.38        14.70        39.95        29.23        23.74 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       23.97        12.92         7.00 

$`AMP PEAK 33(13Q34) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
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-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 
        7.92         9.60         8.02        91.04        46.32         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33        14.96        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         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-A3NH 
       17.06        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         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        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        20.91       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-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       46.78        49.15        30.90        10.42        27.85        16.24 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        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-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-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        30.12        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        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 
       27.29        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-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-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       33.11        14.27        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        22.06        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 
       20.02        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-A4ZD TCGA-BK-A56F TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TC 
       16.64        13.18        10.03         9.86        46.95        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-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-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       29.33        32.58        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NZ TCGA-D1-A1O5 
       22.92         1.41        13.22        18.25        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-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       27.32        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS 
       61.74        61.55        66.90        46.26        57.60        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU 
       26.43        35.15        17.19        27.16        17.88        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-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        11.08         6.48        19.33 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       10.19        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       29.10        13.84        17.92        14.14        19.89        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         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-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        41.06        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE 
                        0.56                         0.07 
  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 
                       20.28                        23.38 
[1] "0.6 - 125.4 (20.3)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.3"
D33V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 33(13Q34) MUTATED                                        14
  AMP PEAK 33(13Q34) WILD-TYPE                                     381
                              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                                  39
  AMP PEAK 33(13Q34) WILD-TYPE                                73
D33V3, multiclass
                                         clus
vv                                        AMP PEAK 33(13Q34) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         14
  MIXED SEROUS AND ENDOMETRIOID                                    4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               39
                                         clus
vv                                        AMP PEAK 33(13Q34) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          381
  MIXED SEROUS AND ENDOMETRIOID                                     17
  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"
D33V4, binary
                              cls
clus                             0   1
  AMP PEAK 33(13Q34) MUTATED    16  41
  AMP PEAK 33(13Q34) WILD-TYPE 125 346
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(13Q34) MUTATED     16   41
  AMP PEAK 33(13Q34) WILD-TYPE  125  346
     clus
vv    AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE
  NO                          16                          125
  YES                         41                          346
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 33(13Q34) MUTATED    34   6   4   6
  AMP PEAK 33(13Q34) WILD-TYPE 329  17  13  29
D33V5, multiclass
    clus
vv   AMP PEAK 33(13Q34) MUTATED AMP PEAK 33(13Q34) WILD-TYPE
  R0                         34                          329
  R1                          6                           17
  R2                          4                           13
  RX                          6                           29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 33(13Q34) MUTATED                                  0     2
  AMP PEAK 33(13Q34) WILD-TYPE                                4    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 33(13Q34) MUTATED                          18
  AMP PEAK 33(13Q34) WILD-TYPE                        83
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 33(13Q34) MUTATED                                           2    32
  AMP PEAK 33(13Q34) WILD-TYPE                                         7   334
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                                                             32
                                           clus
vv                                          AMP PEAK 33(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  WHITE                                                              334
[1] 5 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  38
  AMP PEAK 33(13Q34) WILD-TYPE  13 329
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 33(13Q34) MUTATED      1   38
  AMP PEAK 33(13Q34) WILD-TYPE   13  329
                        clus
vv                       AMP PEAK 33(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         38
                        clus
vv                       AMP PEAK 33(13Q34) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          329
[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  19
  AMP PEAK 34(14Q24.3) WILD-TYPE 413  50
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            63                            463 
  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                            19                             50 
$`AMP PEAK 34(14Q24.3) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GR TCGA-A5-A1OH TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 
       36.69        36.82        36.33         8.02        91.04        28.64 
TCGA-A5-A3LP TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AP-A053 
       14.96         1.64        22.26        20.81        21.21         5.95 
TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 
       63.91        36.89       125.42        97.71        46.78        21.90 
TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2HF TCGA-AX-A2IO 
       37.78        12.43        11.08        30.12        19.36        64.93 
TCGA-AX-A3FX TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0K3 TCGA-B5-A0K4 TCGA-B5-A1MU 
       43.82         0.39        56.91        27.29        17.88        50.89 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       15.45         6.81        35.90        24.13        16.64        67.20 
TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NX TCGA-D1-A1O0 
       22.55        37.32        11.51        14.73        18.25         2.07 
TCGA-D1-A2G5 TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3B1 
       41.42       110.10        17.06        10.92        51.52        26.96 
TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EW 
        4.54        11.08        10.19        11.38        39.95        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KP-A3VZ 
        9.07        28.93        29.23        41.06        14.04        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A7D5 
       13.28        18.21        23.97 

$`AMP PEAK 34(14Q24.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
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-A1OJ TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
       11.44         9.60        46.32         5.33         5.16         7.33 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM 
        1.18        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.68        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         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-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       45.53        23.87        12.20        20.91        48.79       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-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-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        36.13         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-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-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       36.39         4.77        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 
       31.13         0.23         0.20         0.56         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        80.38        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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       22.06        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-A0CA 
        9.57        20.02        23.70        20.12        11.31        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F 
        6.21        10.22        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-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-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
        1.41        13.22         0.72        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95         3.52         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        4.27         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        23.38        48.36         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       27.32        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        57.60        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-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-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       20.05        45.76        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        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       96.69        28.96        25.02        45.01         1.74         7.76 
TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
        2.43         9.47        26.10        23.24        15.45        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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE 
                          0.39                           0.07 
  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 
                         23.74                          23.34 
[1] "0.4 - 125.4 (23.7)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.7"
D34V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 34(14Q24.3) MUTATED                                        21
  AMP PEAK 34(14Q24.3) WILD-TYPE                                     374
                                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                                  38
  AMP PEAK 34(14Q24.3) WILD-TYPE                                74
D34V3, multiclass
                                         clus
vv                                        AMP PEAK 34(14Q24.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           21
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        AMP PEAK 34(14Q24.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            374
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                                cls
clus                               0   1
  AMP PEAK 34(14Q24.3) MUTATED    12  51
  AMP PEAK 34(14Q24.3) WILD-TYPE 129 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(14Q24.3) MUTATED     12   51
  AMP PEAK 34(14Q24.3) WILD-TYPE  129  336
     clus
vv    AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE
  NO                            12                            129
  YES                           51                            336
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 34(14Q24.3) MUTATED    42   4   2   7
  AMP PEAK 34(14Q24.3) WILD-TYPE 321  19  15  28
D34V5, multiclass
    clus
vv   AMP PEAK 34(14Q24.3) MUTATED AMP PEAK 34(14Q24.3) WILD-TYPE
  R0                           42                            321
  R1                            4                             19
  R2                            2                             15
  RX                            7                             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 34(14Q24.3) MUTATED                                  0     0
  AMP PEAK 34(14Q24.3) WILD-TYPE                                4    20
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 34(14Q24.3) MUTATED                          10
  AMP PEAK 34(14Q24.3) WILD-TYPE                        91
                                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      48
  AMP PEAK 34(14Q24.3) WILD-TYPE   318
D34V6, multiclass
                                           clus
vv                                          AMP PEAK 34(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               48
                                           clus
vv                                          AMP PEAK 34(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 20
  BLACK OR AFRICAN AMERICAN                                             91
  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"
D34V7, binary
                                cls
clus                               0   1
  AMP PEAK 34(14Q24.3) MUTATED     2  44
  AMP PEAK 34(14Q24.3) WILD-TYPE  12 323
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 34(14Q24.3) MUTATED      2   44
  AMP PEAK 34(14Q24.3) WILD-TYPE   12  323
                        clus
vv                       AMP PEAK 34(14Q24.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       AMP PEAK 34(14Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            323
[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    57  18
  AMP PEAK 35(14Q32.33) WILD-TYPE 400  51
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             75                             451 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                             18                              51 
$`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        20.81        16.87 
TCGA-AP-A05A TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       63.91        48.79        97.71        21.90        36.13         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        43.82 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0K4 TCGA-B5-A0KB 
        0.26         0.39        80.38        56.91        17.88         4.11 
TCGA-B5-A1MU TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP 
       50.89        33.11        34.95        36.49        15.45         6.81 
TCGA-BK-A0C9 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       35.90        24.13        16.64        67.20        49.55        22.55 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A2G7 
       37.32        11.51        18.67         2.07        41.42        44.88 
TCGA-D1-A3DG TCGA-DI-A2QY TCGA-E6-A1M0 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y 
        4.27       110.10        17.06        49.15        37.71        51.52 
TCGA-EO-A3B1 TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
       26.96         4.54        23.90        11.08        12.59        10.19 
TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW 
       20.05        27.35        11.38        14.70        39.95        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
        9.07        28.93        41.06         1.74         7.76        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A914 
       13.28        18.21        12.92 

$`AMP PEAK 35(14Q32.33) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        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 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16         0.76        18.90         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        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 
       45.53        36.89        23.87        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        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       10.42        27.85        16.24        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-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-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         1.38         0.30         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        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        27.29 
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-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-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       12.79       116.25        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98        22.06        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        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       11.31        34.98         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-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-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-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-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.11        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        31.10        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-A22R 
       27.32        16.04         7.36        16.80        10.92        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
       53.88        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-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       14.40        18.87        22.82        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       13.84        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KJ-A3U4 
       96.69        28.96        25.02        29.23        45.01         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       23.74         9.47        26.10        23.24        15.45        23.97 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                           0.26                            0.07 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                         110.10                          191.84 
  AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE 
                          23.90                           23.34 
[1] "0.3 - 110.1 (23.9)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.2"
D35V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 35(14Q32.33) MUTATED                                        30
  AMP PEAK 35(14Q32.33) WILD-TYPE                                     365
                                 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                                  41
  AMP PEAK 35(14Q32.33) WILD-TYPE                                71
D35V3, multiclass
                                         clus
vv                                        AMP PEAK 35(14Q32.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            30
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  41
                                         clus
vv                                        AMP PEAK 35(14Q32.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             365
  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"
D35V4, binary
                                 cls
clus                                0   1
  AMP PEAK 35(14Q32.33) MUTATED    11  65
  AMP PEAK 35(14Q32.33) WILD-TYPE 130 322
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(14Q32.33) MUTATED     11   65
  AMP PEAK 35(14Q32.33) WILD-TYPE  130  322
     clus
vv    AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE
  NO                             11                             130
  YES                            65                             322
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 35(14Q32.33) MUTATED    49   4   4   7
  AMP PEAK 35(14Q32.33) WILD-TYPE 314  19  13  28
D35V5, multiclass
    clus
vv   AMP PEAK 35(14Q32.33) MUTATED AMP PEAK 35(14Q32.33) WILD-TYPE
  R0                            49                             314
  R1                             4                              19
  R2                             4                              13
  RX                             7                              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 35(14Q32.33) MUTATED                                  0     0
  AMP PEAK 35(14Q32.33) WILD-TYPE                                4    20
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 35(14Q32.33) MUTATED                          23
  AMP PEAK 35(14Q32.33) WILD-TYPE                        78
                                 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      46
  AMP PEAK 35(14Q32.33) WILD-TYPE   320
D35V6, multiclass
                                           clus
vv                                          AMP PEAK 35(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 0
  BLACK OR AFRICAN AMERICAN                                            23
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                                46
                                           clus
vv                                          AMP PEAK 35(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  20
  BLACK OR AFRICAN AMERICAN                                              78
  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"
D35V7, binary
                                 cls
clus                                0   1
  AMP PEAK 35(14Q32.33) MUTATED     1  55
  AMP PEAK 35(14Q32.33) WILD-TYPE  13 312
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 35(14Q32.33) MUTATED      1   55
  AMP PEAK 35(14Q32.33) WILD-TYPE   13  312
                        clus
vv                       AMP PEAK 35(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            55
                        clus
vv                       AMP PEAK 35(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             312
[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    25  12
  AMP PEAK 36(15Q26.3) WILD-TYPE 432  57
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            37                            489 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                            12                             57 
$`AMP PEAK 36(15Q26.3) MUTATED`
TCGA-AJ-A3BD TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A1C7 
       34.16        20.81        10.19        97.71        46.78        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        46.49        19.36 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A11I TCGA-BG-A0M8 TCGA-BK-A0CC TCGA-BS-A0TE 
       43.82        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       110.10        17.06 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A72D TCGA-FI-A2CX 
       51.42        34.39         4.54        11.08         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        23.24        12.92 
TCGA-QS-A8F1 
        4.44 

$`AMP PEAK 36(15Q26.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        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-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP 
       19.96        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-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-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
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        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        63.91        57.80        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       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-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-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        21.90        36.13         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-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-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       20.28        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       25.12        36.39         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       34.32        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 
       64.93         0.23         0.20         0.56         0.20         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        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-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-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 
       20.94        35.21        34.98        22.06        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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         6.81        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        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-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-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX 
       36.62        24.30         9.37        12.39        31.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       48.36         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
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-A1GX TCGA-EY-A1H0 
       15.09        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       12.59        10.19        14.40        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       45.76        31.04        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CY 
       17.92        14.14        19.89        14.70        16.96        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-JU-AAVI 
       59.01         9.07        28.96        25.02        29.23         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       18.21        15.45        23.97         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                          1.74                           0.07 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                        110.10                         191.84 
  AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE 
                         28.08                          23.31 
[1] "1.7 - 110.1 (28.1)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.7"
D36V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 36(15Q26.3) MUTATED                                        17
  AMP PEAK 36(15Q26.3) WILD-TYPE                                     378
                                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                                  19
  AMP PEAK 36(15Q26.3) WILD-TYPE                                93
D36V3, multiclass
                                         clus
vv                                        AMP PEAK 36(15Q26.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           17
  MIXED SEROUS AND ENDOMETRIOID                                      1
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 19
                                         clus
vv                                        AMP PEAK 36(15Q26.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            378
  MIXED SEROUS AND ENDOMETRIOID                                       20
  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"
D36V4, binary
                                cls
clus                               0   1
  AMP PEAK 36(15Q26.3) MUTATED     5  32
  AMP PEAK 36(15Q26.3) WILD-TYPE 136 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(15Q26.3) MUTATED      5   32
  AMP PEAK 36(15Q26.3) WILD-TYPE  136  355
     clus
vv    AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE
  NO                             5                            136
  YES                           32                            355
[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 343  20  13  31
D36V5, multiclass
    clus
vv   AMP PEAK 36(15Q26.3) MUTATED AMP PEAK 36(15Q26.3) WILD-TYPE
  R0                           20                            343
  R1                            3                             20
  R2                            4                             13
  RX                            4                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 36(15Q26.3) MUTATED                                  0     2
  AMP PEAK 36(15Q26.3) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 36(15Q26.3) MUTATED                           9
  AMP PEAK 36(15Q26.3) WILD-TYPE                        92
                                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   341
D36V6, multiclass
                                           clus
vv                                          AMP PEAK 36(15Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                            9
  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                                                                 18
  BLACK OR AFRICAN AMERICAN                                             92
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              9
  WHITE                                                                341
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                                cls
clus                               0   1
  AMP PEAK 36(15Q26.3) MUTATED     2  31
  AMP PEAK 36(15Q26.3) WILD-TYPE  12 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 36(15Q26.3) MUTATED      2   31
  AMP PEAK 36(15Q26.3) WILD-TYPE   12  336
                        clus
vv                       AMP PEAK 36(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       AMP PEAK 36(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            336
[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    50  14
  AMP PEAK 37(16P11.2) WILD-TYPE 407  55
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            64                            462 
  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                            14                             55 
$`AMP PEAK 37(16P11.2) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23N 
       36.69        65.75        11.44        91.04        14.96        14.43 
TCGA-AJ-A3BD TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A1DQ TCGA-AP-A3K1 
       34.16        21.99        57.80        36.89        46.78        21.90 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A2H5 TCGA-AX-A3G1 
       28.54        37.78        16.96        20.28        71.24        20.52 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11V TCGA-B5-A1MS 
        0.39        80.38        17.85        75.72        19.56       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A3PP 
       11.87        12.79        22.06        36.49        24.39         6.81 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A102 TCGA-D1-A168 TCGA-D1-A16G 
       10.22        24.13        67.20         4.44        36.10        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16S TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1NX 
       11.51        29.92        18.67        28.08         0.72        18.25 
TCGA-D1-A3DH TCGA-DI-A2QU TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
        4.11        31.10        49.15        37.71        51.42        19.40 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2OQ 
       22.26        16.34         4.54        11.08        10.19        29.10 
TCGA-EY-A3L3 TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A3PX 
       27.35        17.92        14.70         5.88        39.95        45.01 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       23.97        12.92         7.00         0.07 

$`AMP PEAK 37(16P11.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        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-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        46.32        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.16         7.33         1.18        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
       29.39         2.40        34.36         1.12         0.76        18.90 
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        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH 
       20.81        36.99        20.65        21.21        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       12.82        20.78         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-A05N 
       23.31        86.07         8.22        63.91        45.53        23.87 
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-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-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        36.13         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-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-A1CC TCGA-AX-A1CE TCGA-AX-A1CF 
       19.20        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-A1CR 
       72.56        54.12        67.50        25.12        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
        4.77        30.12        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        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        27.29        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-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-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      191.84        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-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX 
       29.65        41.06        34.13        34.95        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        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-A0VV 
       39.32        30.81        21.17        20.28        15.42        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        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98         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-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-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16N TCGA-D1-A16O 
       37.32        36.36        37.51        36.79        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41        13.22        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-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27        16.93        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       12.39       110.10        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        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       34.39        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        14.53        24.89         6.21        14.99        53.88 
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-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-A2ON TCGA-EY-A2OO 
       12.59        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       31.04        13.84        11.38        14.14        19.89        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         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-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       29.23        41.06         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       23.74        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        14.07        18.28         0.23 

  AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE 
                          0.07                           0.13 
  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 
                        22.025                         23.425 
[1] "0.1 - 102.3 (22.0)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2"  
D37V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 37(16P11.2) MUTATED                                        22
  AMP PEAK 37(16P11.2) WILD-TYPE                                     373
                                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                                72
D37V3, multiclass
                                         clus
vv                                        AMP PEAK 37(16P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           22
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 40
                                         clus
vv                                        AMP PEAK 37(16P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            373
  MIXED SEROUS AND ENDOMETRIOID                                       19
  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"
D37V4, binary
                                cls
clus                               0   1
  AMP PEAK 37(16P11.2) MUTATED    14  50
  AMP PEAK 37(16P11.2) WILD-TYPE 127 337
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(16P11.2) MUTATED     14   50
  AMP PEAK 37(16P11.2) WILD-TYPE  127  337
     clus
vv    AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE
  NO                            14                            127
  YES                           50                            337
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 37(16P11.2) MUTATED    40   3   3   9
  AMP PEAK 37(16P11.2) WILD-TYPE 323  20  14  26
D37V5, multiclass
    clus
vv   AMP PEAK 37(16P11.2) MUTATED AMP PEAK 37(16P11.2) WILD-TYPE
  R0                           40                            323
  R1                            3                             20
  R2                            3                             14
  RX                            9                             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 37(16P11.2) MUTATED                                  0     2
  AMP PEAK 37(16P11.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 37(16P11.2) MUTATED                          20
  AMP PEAK 37(16P11.2) WILD-TYPE                        81
                                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   330
D37V6, multiclass
                                           clus
vv                                          AMP PEAK 37(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           20
  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                                                                 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"
D37V7, binary
                                cls
clus                               0   1
  AMP PEAK 37(16P11.2) MUTATED     2  46
  AMP PEAK 37(16P11.2) WILD-TYPE  12 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 37(16P11.2) MUTATED      2   46
  AMP PEAK 37(16P11.2) WILD-TYPE   12  321
                        clus
vv                       AMP PEAK 37(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       AMP PEAK 37(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            321
[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    55  16
  AMP PEAK 38(17Q11.2) WILD-TYPE 402  53
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            71                            455 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                            16                             53 
$`AMP PEAK 38(17Q11.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH 
       41.06        36.69        37.02        17.59        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3EJ 
       91.04        28.64        14.96         1.18        34.16         1.64 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0LI 
       10.19        16.87        63.91        57.80        36.89        97.71 
TCGA-AP-A5FX TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H2 
       36.13        13.28        16.96        13.55        36.39         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3G7 TCGA-AX-A3GI 
       30.12        71.24        17.75         2.96         0.30         0.39 
TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FB 
       27.29         4.11        75.72        11.87        12.79        78.81 
TCGA-B5-A3S1 TCGA-BG-A0M4 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BS-A0U9 
       29.65        34.98        12.56         6.81        10.22        67.20 
TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A3DA TCGA-DI-A1NN 
       49.55        29.95         0.72         2.07         0.26        35.38 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CH TCGA-EO-A3B1 
       12.39       110.10        27.32        10.92        19.40        26.96 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A210 
       16.34        23.90         6.90        19.27        15.09        12.59 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EX 
       20.05        29.10        13.84        11.38        39.95         9.07 
TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-PG-A915 TCGA-SL-A6J9 
       45.01        14.04         2.43         7.00         0.07 

$`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 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79        29.39         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76        18.90         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 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         2.70         0.13        83.67        21.99         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        45.53        23.87        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-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        46.78 
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 
       21.90         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-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-A2H7 
       72.56        54.12        67.50        25.12        11.08        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
       43.82         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47        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-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-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-A3FC 
       14.70        11.70        15.29       116.25        96.30        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       33.11        14.27        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M6 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        22.06        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-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         6.21 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        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-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-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-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-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-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         4.27         4.11        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        31.10        23.38        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        16.04         7.36        16.80        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        22.26        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       22.78        13.97        18.84        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       12.43        15.81        11.08         6.48        19.33        10.19 
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-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
       96.69        59.01        28.93        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
       41.06         1.74         7.76        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        18.21        23.24        15.45        23.97        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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.23 

  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                          0.07                           0.13 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                        110.10                         191.84 
  AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE 
                         17.59                          23.64 
[1] "0.1 - 110.1 (17.6)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.4"
D38V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 38(17Q11.2) MUTATED                                        19
  AMP PEAK 38(17Q11.2) WILD-TYPE                                     376
                                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                                66
D38V3, multiclass
                                         clus
vv                                        AMP PEAK 38(17Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           19
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 46
                                         clus
vv                                        AMP PEAK 38(17Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            376
  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"
D38V4, binary
                                cls
clus                               0   1
  AMP PEAK 38(17Q11.2) MUTATED    15  56
  AMP PEAK 38(17Q11.2) WILD-TYPE 126 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(17Q11.2) MUTATED     15   56
  AMP PEAK 38(17Q11.2) WILD-TYPE  126  331
     clus
vv    AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE
  NO                            15                            126
  YES                           56                            331
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 38(17Q11.2) MUTATED    39   7   6   7
  AMP PEAK 38(17Q11.2) WILD-TYPE 324  16  11  28
D38V5, multiclass
    clus
vv   AMP PEAK 38(17Q11.2) MUTATED AMP PEAK 38(17Q11.2) WILD-TYPE
  R0                           39                            324
  R1                            7                             16
  R2                            6                             11
  RX                            7                             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 38(17Q11.2) MUTATED                                  1     1
  AMP PEAK 38(17Q11.2) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 38(17Q11.2) MUTATED                          25
  AMP PEAK 38(17Q11.2) WILD-TYPE                        76
                                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   328
D38V6, multiclass
                                           clus
vv                                          AMP PEAK 38(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           25
  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                                                                 19
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  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"
D38V7, binary
                                cls
clus                               0   1
  AMP PEAK 38(17Q11.2) MUTATED     3  46
  AMP PEAK 38(17Q11.2) WILD-TYPE  11 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 38(17Q11.2) MUTATED      3   46
  AMP PEAK 38(17Q11.2) WILD-TYPE   11  321
                        clus
vv                       AMP PEAK 38(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           46
                        clus
vv                       AMP PEAK 38(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            321
[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    56  18
  AMP PEAK 39(17Q12) WILD-TYPE 401  51
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          74                          452 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                          18                           51 
$`AMP PEAK 39(17Q12) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GR TCGA-A5-A1OH TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3NH 
       41.06        36.82        36.33         1.18        34.16        10.19 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05H 
       16.87        16.87        20.78         5.95        63.91        45.53 
TCGA-AP-A0LH TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C4 TCGA-AX-A1C7 TCGA-AX-A1CF 
       36.36        28.54        37.78        13.28        16.96        76.83 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2HK 
       36.39        11.08         4.77        19.36        17.75         2.96 
TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 
       64.93        43.82         0.26         0.39        80.38        27.29 
TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       75.72        11.87        12.79        29.65        34.13        34.95 
TCGA-BG-A0M2 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BK-A26L TCGA-BS-A0U8 TCGA-D1-A0ZP 
       20.94        34.98        22.06        24.13        97.41        29.95 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NX TCGA-D1-A2G0 TCGA-D1-A3JP 
       27.42        11.51        18.67        18.25         3.52        16.93 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A3B1 
       35.38        12.39       110.10        48.36        27.32        26.96 
TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A2ON 
        4.54        19.27        17.62        15.09        10.19        20.05 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2EX TCGA-FI-A2EY 
       27.35        13.84        11.38        14.70         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W4 
       25.02        29.23        45.01         7.76         2.43        18.21 
TCGA-PG-A915 TCGA-SL-A6J9 
        7.00         0.07 

$`AMP PEAK 39(17Q12) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 
       11.44         9.60         8.02        91.04        46.32        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        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79        29.39         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        57.80        36.89        23.87        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        46.78        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        21.90 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       36.13         0.56        13.58        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-A1C5 TCGA-AX-A1C8 
       35.01        43.82        40.11        65.88        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-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN 
       81.37        34.32        46.49        26.33        30.74        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.23         0.20         0.56         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR 
        0.30         0.30         1.18        18.35        14.47        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       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-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-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-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        41.06 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M3 TCGA-BG-A0M7 TCGA-BG-A0M8 
       18.61        20.19        19.33        35.21        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-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
        6.21        10.22        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-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       30.74        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-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-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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22         0.72        16.87        18.02 
TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 
        2.07        15.06         1.05         3.95        41.42         8.48 
TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.27         4.11        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-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        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-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-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 
       16.11        12.43        15.81        11.08         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-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       29.10        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR 
        8.98        96.69        59.01        28.96        41.06         1.74 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC 
       14.04        23.74        13.28         9.47        26.10        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       15.45        23.97        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                        0.07                         0.13 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                      110.10                       191.84 
  AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE 
                      20.415                       23.470 
[1] "0.1 - 110.1 (20.4)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.6"
D39V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 39(17Q12) MUTATED                                        20
  AMP PEAK 39(17Q12) WILD-TYPE                                     375
                              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                                  51
  AMP PEAK 39(17Q12) WILD-TYPE                                61
D39V3, multiclass
                                         clus
vv                                        AMP PEAK 39(17Q12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         20
  MIXED SEROUS AND ENDOMETRIOID                                    3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               51
                                         clus
vv                                        AMP PEAK 39(17Q12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          375
  MIXED SEROUS AND ENDOMETRIOID                                     18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V4, binary
                              cls
clus                             0   1
  AMP PEAK 39(17Q12) MUTATED    20  54
  AMP PEAK 39(17Q12) WILD-TYPE 121 333
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 39(17Q12) MUTATED     20   54
  AMP PEAK 39(17Q12) WILD-TYPE  121  333
     clus
vv    AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE
  NO                          20                          121
  YES                         54                          333
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 39(17Q12) MUTATED    46   5   4   6
  AMP PEAK 39(17Q12) WILD-TYPE 317  18  13  29
D39V5, multiclass
    clus
vv   AMP PEAK 39(17Q12) MUTATED AMP PEAK 39(17Q12) WILD-TYPE
  R0                         46                          317
  R1                          5                           18
  R2                          4                           13
  RX                          6                           29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 39(17Q12) MUTATED                                  1     0
  AMP PEAK 39(17Q12) WILD-TYPE                                3    20
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 39(17Q12) MUTATED                          25
  AMP PEAK 39(17Q12) WILD-TYPE                        76
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 39(17Q12) MUTATED                                           0    47
  AMP PEAK 39(17Q12) WILD-TYPE                                         9   319
D39V6, multiclass
                                           clus
vv                                          AMP PEAK 39(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              0
  BLACK OR AFRICAN AMERICAN                                         25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          0
  WHITE                                                             47
                                           clus
vv                                          AMP PEAK 39(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               20
  BLACK OR AFRICAN AMERICAN                                           76
  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"
D39V7, binary
                              cls
clus                             0   1
  AMP PEAK 39(17Q12) MUTATED     2  57
  AMP PEAK 39(17Q12) WILD-TYPE  12 310
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 39(17Q12) MUTATED      2   57
  AMP PEAK 39(17Q12) WILD-TYPE   12  310
                        clus
vv                       AMP PEAK 39(17Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         57
                        clus
vv                       AMP PEAK 39(17Q12) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          310
[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    78  24
  AMP PEAK 40(17Q25.1) WILD-TYPE 379  45
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                           102                            424 
  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                            24                             45 
$`AMP PEAK 40(17Q25.1) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH 
       41.06        36.69        65.75        36.82        17.59        36.33 
TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3EM 
       28.64         1.18        14.43        34.16         1.12        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 
       20.81        10.19        16.87        20.78        21.99         5.95 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH 
       63.91        57.80        36.89        48.79       125.42        36.36 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW 
       21.90        36.13         0.56        53.92        28.54        37.78 
TCGA-AX-A1C4 TCGA-AX-A1CF TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2HF 
       13.28        76.83        25.12        11.08         4.77        19.36 
TCGA-AX-A2HH TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       17.75         2.96         0.56        43.82        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.26         0.39        80.38        27.29        17.85         4.11 
TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-BG-A0M2 TCGA-BG-A0M4 
       75.72       102.31        11.87        12.79        20.94        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-BS-A0TI 
       22.06        36.49         6.81        10.22        16.64        61.87 
TCGA-BS-A0U9 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16S 
       67.20        29.95        22.55        39.48        11.51        18.67 
TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3JP TCGA-DI-A1NN 
        0.72         2.07         3.52        44.88        16.93        35.38 
TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A3AS TCGA-EO-A3KU 
        9.37       110.10        48.36        27.32        34.39        22.26 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A210 
       16.34        23.90         6.90        19.27        15.09        12.59 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CY 
       20.05        29.10        27.35        11.38        14.70        41.06 
TCGA-FI-A2EU TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       96.69        29.23        45.01         1.74         7.76        14.04 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A915 TCGA-SL-A6J9 
       23.74         9.47        18.21        23.97         7.00         0.07 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.95        14.76        16.87        22.32        12.82         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H 
        0.13        83.67        23.31        86.07         8.22        45.53 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        12.20        20.91       117.99       110.37         3.39 
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-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ 
       71.67        60.36        55.89        31.30        35.54        46.78 
TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 
       49.15         6.71        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-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-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C5 TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        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-A1CP 
       12.43        20.05        72.56        54.12        67.50        36.39 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       30.12        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       46.49        26.33        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.20         1.38         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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-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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        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-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-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 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        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-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-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-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-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-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-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-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV 
       41.42         8.48         0.26         4.27         4.11        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-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 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        19.40        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        26.96        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       22.78        13.97        18.84        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       12.43        15.81        11.08         6.48        19.33        10.19 
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-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       17.92        14.14        19.89        16.96         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW 
       39.88        39.95         7.99        13.84         8.98        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KJ-A3U4 
        9.07        28.93        28.96        25.02        41.06         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
       13.28        26.10        23.24        15.45        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE 
                          0.07                           0.13 
  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 
                        21.420                         23.785 
[1] "0.1 - 125.4 (21.4)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2.5"
D40V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 40(17Q25.1) MUTATED                                        37
  AMP PEAK 40(17Q25.1) WILD-TYPE                                     358
                                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                                  56
  AMP PEAK 40(17Q25.1) WILD-TYPE                                56
D40V3, multiclass
                                         clus
vv                                        AMP PEAK 40(17Q25.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           37
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 56
                                         clus
vv                                        AMP PEAK 40(17Q25.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            358
  MIXED SEROUS AND ENDOMETRIOID                                       12
  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"
D40V4, binary
                                cls
clus                               0   1
  AMP PEAK 40(17Q25.1) MUTATED    24  78
  AMP PEAK 40(17Q25.1) WILD-TYPE 117 309
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(17Q25.1) MUTATED     24   78
  AMP PEAK 40(17Q25.1) WILD-TYPE  117  309
     clus
vv    AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE
  NO                            24                            117
  YES                           78                            309
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 40(17Q25.1) MUTATED    65   4   5  11
  AMP PEAK 40(17Q25.1) WILD-TYPE 298  19  12  24
D40V5, multiclass
    clus
vv   AMP PEAK 40(17Q25.1) MUTATED AMP PEAK 40(17Q25.1) WILD-TYPE
  R0                           65                            298
  R1                            4                             19
  R2                            5                             12
  RX                           11                             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 40(17Q25.1) MUTATED                                  0     0
  AMP PEAK 40(17Q25.1) WILD-TYPE                                4    20
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 40(17Q25.1) MUTATED                          36
  AMP PEAK 40(17Q25.1) WILD-TYPE                        65
                                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      59
  AMP PEAK 40(17Q25.1) WILD-TYPE   307
D40V6, multiclass
                                           clus
vv                                          AMP PEAK 40(17Q25.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           36
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               59
                                           clus
vv                                          AMP PEAK 40(17Q25.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 20
  BLACK OR AFRICAN AMERICAN                                             65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  WHITE                                                                307
[1] 5 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  76
  AMP PEAK 40(17Q25.1) WILD-TYPE  13 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 40(17Q25.1) MUTATED      1   76
  AMP PEAK 40(17Q25.1) WILD-TYPE   13  291
                        clus
vv                       AMP PEAK 40(17Q25.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       AMP PEAK 40(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            291
[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    73  21
  AMP PEAK 41(18P11.31) WILD-TYPE 384  48
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             94                             432 
  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                             21                              48 
$`AMP PEAK 41(18P11.31) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GE TCGA-A5-A0GR TCGA-A5-A0R6 
       41.06        36.69        37.02       105.37        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3EM 
       11.44        36.33        14.96        14.43        34.16        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       20.81        21.21        10.19        16.87        16.87        20.78 
TCGA-AP-A05A TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO 
       63.91        48.79       125.42         3.39        97.71        33.40 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A0IW TCGA-AX-A1C9 TCGA-AX-A1CA 
       46.78        21.90        36.13        37.78        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 
       12.43        76.83         4.77        30.12        71.24        61.18 
TCGA-AX-A2HC TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G3 
       34.32         2.96        64.93         0.56        43.82         1.38 
TCGA-AX-A3GI TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A3S1 TCGA-B5-A5OD 
        0.39        17.85         4.11        75.72        29.65        34.13 
TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A2AE TCGA-BK-A0CC 
       34.95        22.06        36.49        24.39        23.70        10.22 
TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A1NW 
       24.13        67.20        39.48        37.32        18.67         0.72 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO 
        3.52        44.88         4.11        16.93        35.38         9.37 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ 
      110.10        48.36        27.32        51.42        19.40        27.16 
TCGA-EO-A3KU TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ 
       22.26        17.62        12.59        10.19        20.05        29.10 
TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       17.92         5.88        41.06        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W1 
       25.02        29.23        45.01        14.04         2.43         9.47 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       23.24        23.97         7.00         4.44 

$`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 
       10.29       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 
      112.54        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        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79        29.39         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       14.76        22.32        12.82         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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       45.53        36.89        23.87        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-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-AW-A1PO 
        6.71        30.90        10.42        27.85        16.24         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-A1C7 
       43.82        40.11        65.88        13.28        19.20        16.96 
TCGA-AX-A1C8 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN 
       13.55        20.05        72.56        54.12        67.50        25.12 
TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF 
       36.39        11.08        40.80        81.37        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13         0.23         0.20 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        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        27.29        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-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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW 
       78.81        62.14        33.11        14.27        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-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-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        20.02        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-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-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-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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
       13.22        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG 
        1.05         3.95        41.42         8.48         0.26         4.27 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30        12.39        31.10        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.52        34.39        26.43        35.15        17.19        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       26.96        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        15.09        16.11        12.43        15.81        11.08 
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-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       31.04        27.35        13.84        11.38        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       14.70        16.96        40.01        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR 
       13.84         8.98        96.69        28.96        41.06         1.74 
TCGA-JU-AAVI TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
        7.76        23.74        13.28        26.10        18.21        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE 
                           0.39                            0.07 
  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 
                         23.835                          23.325 
[1] "0.4 - 125.4 (23.8)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2"  
D41V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 41(18P11.31) MUTATED                                        29
  AMP PEAK 41(18P11.31) WILD-TYPE                                     366
                                 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                                  59
  AMP PEAK 41(18P11.31) WILD-TYPE                                53
D41V3, multiclass
                                         clus
vv                                        AMP PEAK 41(18P11.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            29
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  59
                                         clus
vv                                        AMP PEAK 41(18P11.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             366
  MIXED SEROUS AND ENDOMETRIOID                                        15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V4, binary
                                 cls
clus                                0   1
  AMP PEAK 41(18P11.31) MUTATED    16  78
  AMP PEAK 41(18P11.31) WILD-TYPE 125 309
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 41(18P11.31) MUTATED     16   78
  AMP PEAK 41(18P11.31) WILD-TYPE  125  309
     clus
vv    AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE
  NO                             16                             125
  YES                            78                             309
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 41(18P11.31) MUTATED    61   3   8   7
  AMP PEAK 41(18P11.31) WILD-TYPE 302  20   9  28
D41V5, multiclass
    clus
vv   AMP PEAK 41(18P11.31) MUTATED AMP PEAK 41(18P11.31) WILD-TYPE
  R0                            61                             302
  R1                             3                              20
  R2                             8                               9
  RX                             7                              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 41(18P11.31) MUTATED                                  0     3
  AMP PEAK 41(18P11.31) WILD-TYPE                                4    17
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 41(18P11.31) MUTATED                          33
  AMP PEAK 41(18P11.31) WILD-TYPE                        68
                                 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      52
  AMP PEAK 41(18P11.31) WILD-TYPE   314
D41V6, multiclass
                                           clus
vv                                          AMP PEAK 41(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                            33
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                52
                                           clus
vv                                          AMP PEAK 41(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  17
  BLACK OR AFRICAN AMERICAN                                              68
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               8
  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"
D41V7, binary
                                 cls
clus                                0   1
  AMP PEAK 41(18P11.31) MUTATED     2  67
  AMP PEAK 41(18P11.31) WILD-TYPE  12 300
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 41(18P11.31) MUTATED      2   67
  AMP PEAK 41(18P11.31) WILD-TYPE   12  300
                        clus
vv                       AMP PEAK 41(18P11.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            67
                        clus
vv                       AMP PEAK 41(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             300
[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  17
  AMP PEAK 42(18Q11.2) WILD-TYPE 406  52
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            68                            458 
  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                            17                             52 
$`AMP PEAK 42(18Q11.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GE TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-AJ-A23N 
       41.06        36.69       105.37        19.96        36.33        14.43 
TCGA-AJ-A2QM TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS 
       29.39        22.26        20.81        21.21        10.19        16.87 
TCGA-AJ-A3TW TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LO 
       16.87        36.89        48.79       125.42         3.39        33.40 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 
       46.78        21.90        36.13        30.12        71.24        61.18 
TCGA-AX-A2HC TCGA-AX-A3G3 TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 
       34.32         1.38        80.38        75.72        11.87        12.79 
TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A2AE 
       29.65        34.13        34.95        36.49        24.39        23.70 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-D1-A0ZZ TCGA-D1-A15V 
        6.81        10.22        24.13        67.20        22.55        39.48 
TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN 
       11.51        18.67         3.52        44.88         4.11        35.38 
TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A3AS TCGA-EO-A3B1 
        9.37       110.10        48.36        27.32        34.39        26.96 
TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       17.62        12.59        10.19        20.05        29.10        27.35 
TCGA-EY-A4KR TCGA-EY-A72D TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F9 TCGA-KP-A3W3 
       11.38         5.88        59.01        28.93        29.23        26.10 
TCGA-KP-A3W4 TCGA-PG-A915 
       18.21         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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
       32.78       112.54        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        10.26         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI 
        2.40        34.36        34.16         1.12         0.76        18.90 
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        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       20.65        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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        63.91        57.80 
TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       45.53        23.87        12.20        20.91       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-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-AW-A1PO 
        6.71        30.90        10.42        27.85        16.24         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-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-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HF 
       11.08         4.77        40.80        81.37        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
        0.39        56.91        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 
       27.29        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-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-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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       33.11        14.27        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-A0M9 
       20.94        35.21        34.98        22.06        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-A0VV 
       39.32        30.81        21.17        20.28        15.42        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-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.16        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-A16J TCGA-D1-A16N 
       36.36        37.51        36.79        27.42        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
       41.42         8.48         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-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 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        19.40        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        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 
       11.08         6.48        19.33        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       45.76        31.04        13.84        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.70        16.96        40.01        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2F4 
        7.99        13.84         8.98        96.69         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        41.06        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB 
        2.43        23.74        13.28         9.47        23.24        15.45 
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 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE 
                          1.38                           0.07 
  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 
                         27.14                          22.87 
[1] "1.4 - 125.4 (27.1)" "0.1 - 191.8 (22.9)"
[1] "hr=" "2.1"
D42V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 42(18Q11.2) MUTATED                                        20
  AMP PEAK 42(18Q11.2) WILD-TYPE                                     375
                                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                                  44
  AMP PEAK 42(18Q11.2) WILD-TYPE                                68
D42V3, multiclass
                                         clus
vv                                        AMP PEAK 42(18Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           20
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 44
                                         clus
vv                                        AMP PEAK 42(18Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            375
  MIXED SEROUS AND ENDOMETRIOID                                       17
  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"
D42V4, binary
                                cls
clus                               0   1
  AMP PEAK 42(18Q11.2) MUTATED    15  53
  AMP PEAK 42(18Q11.2) WILD-TYPE 126 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(18Q11.2) MUTATED     15   53
  AMP PEAK 42(18Q11.2) WILD-TYPE  126  334
     clus
vv    AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE
  NO                            15                            126
  YES                           53                            334
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 42(18Q11.2) MUTATED    43   1   4   8
  AMP PEAK 42(18Q11.2) WILD-TYPE 320  22  13  27
D42V5, multiclass
    clus
vv   AMP PEAK 42(18Q11.2) MUTATED AMP PEAK 42(18Q11.2) WILD-TYPE
  R0                           43                            320
  R1                            1                             22
  R2                            4                             13
  RX                            8                             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 42(18Q11.2) MUTATED                                  0     1
  AMP PEAK 42(18Q11.2) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 42(18Q11.2) MUTATED                          25
  AMP PEAK 42(18Q11.2) WILD-TYPE                        76
                                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      38
  AMP PEAK 42(18Q11.2) WILD-TYPE   328
D42V6, multiclass
                                           clus
vv                                          AMP PEAK 42(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               38
                                           clus
vv                                          AMP PEAK 42(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  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"
D42V7, binary
                                cls
clus                               0   1
  AMP PEAK 42(18Q11.2) MUTATED     1  47
  AMP PEAK 42(18Q11.2) WILD-TYPE  13 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 42(18Q11.2) MUTATED      1   47
  AMP PEAK 42(18Q11.2) WILD-TYPE   13  320
                        clus
vv                       AMP PEAK 42(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       AMP PEAK 42(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            320
[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    76  20
  AMP PEAK 43(19P13.2) WILD-TYPE 381  49
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            96                            430 
  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                            20                             49 
$`AMP PEAK 43(19P13.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OH TCGA-A5-A3LP 
       41.06        36.69        37.02        65.75        36.33        14.96 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF 
       14.43        29.39        18.90         1.64        22.26        21.21 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05H 
       16.87        16.87         0.13         5.95        63.91        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX 
       48.79       125.42         3.39        97.71        46.78        36.13 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A1CR 
       28.54        37.78        16.96        13.55        36.39        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2IO 
        4.77        71.24        40.80        61.18        19.36        64.93 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN 
       20.52         0.30         0.26         0.30         0.39        80.38 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3S1 
       27.29        17.85        75.72       102.31        12.79        29.65 
TCGA-B5-A5OE TCGA-BG-A0VT TCGA-BG-A0YV TCGA-BK-A0CC TCGA-BS-A0V8 TCGA-D1-A0ZP 
       34.95        24.39        12.56        10.22        49.55        29.95 
TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU 
       22.55        11.51        18.67        14.73        28.08        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JP 
        0.72        18.25         2.07        44.88         4.11        16.93 
TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 
       35.38        31.10       110.10        27.32        10.92        37.71 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ 
       51.52        19.40        26.96        22.26        16.34        23.90 
TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
       17.62        12.59        10.19        20.05        29.10        27.35 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX 
       11.38        17.92        41.06        25.02        29.23        45.01 
TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       23.74        26.10        23.97        12.92         7.00         4.44 

$`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 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
      112.54       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        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       34.36        34.16         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        17.06        20.81        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       10.19        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 
       20.78         2.70        83.67        21.99        23.31        86.07 
TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        57.80        36.89        23.87        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-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        21.90         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-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-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-A2H4 TCGA-AX-A2HA 
       72.56        54.12        67.50        25.12        30.12        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        1.38         1.18        18.35        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-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-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-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       62.14        33.11        14.27        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        22.06 
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-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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         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-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-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-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-A3DG TCGA-DF-A2KV TCGA-DF-A2KY 
       41.42         8.48         0.26         4.27        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO 
       27.16        16.31        39.29        36.62        24.30         9.37 
TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       12.39        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 
       16.04         7.36        16.80        49.15        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        51.42        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        17.19        27.16        17.88        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        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-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 
       11.08         6.48        19.33        14.40        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       45.76        31.04        13.84        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       16.96         5.88        40.01        39.88        39.95         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-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.96        41.06         1.74         7.76        14.04         2.43 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 
       13.28         9.47        18.21        23.24        15.45        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE 
                          0.13                           0.07 
  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 
                        23.145                         23.340 
[1] "0.1 - 125.4 (23.1)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.9"
D43V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 43(19P13.2) MUTATED                                        26
  AMP PEAK 43(19P13.2) WILD-TYPE                                     369
                                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                                  64
  AMP PEAK 43(19P13.2) WILD-TYPE                                48
D43V3, multiclass
                                         clus
vv                                        AMP PEAK 43(19P13.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           26
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 64
                                         clus
vv                                        AMP PEAK 43(19P13.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            369
  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"
D43V4, binary
                                cls
clus                               0   1
  AMP PEAK 43(19P13.2) MUTATED    18  79
  AMP PEAK 43(19P13.2) WILD-TYPE 123 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 43(19P13.2) MUTATED     18   79
  AMP PEAK 43(19P13.2) WILD-TYPE  123  308
     clus
vv    AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE
  NO                            18                            123
  YES                           79                            308
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 43(19P13.2) MUTATED    62   6   5   8
  AMP PEAK 43(19P13.2) WILD-TYPE 301  17  12  27
D43V5, multiclass
    clus
vv   AMP PEAK 43(19P13.2) MUTATED AMP PEAK 43(19P13.2) WILD-TYPE
  R0                           62                            301
  R1                            6                             17
  R2                            5                             12
  RX                            8                             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 43(19P13.2) MUTATED                                  0     0
  AMP PEAK 43(19P13.2) WILD-TYPE                                4    20
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 43(19P13.2) MUTATED                          31
  AMP PEAK 43(19P13.2) WILD-TYPE                        70
                                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      58
  AMP PEAK 43(19P13.2) WILD-TYPE   308
D43V6, multiclass
                                           clus
vv                                          AMP PEAK 43(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               58
                                           clus
vv                                          AMP PEAK 43(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 20
  BLACK OR AFRICAN AMERICAN                                             70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  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"
D43V7, binary
                                cls
clus                               0   1
  AMP PEAK 43(19P13.2) MUTATED     2  70
  AMP PEAK 43(19P13.2) WILD-TYPE  12 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 43(19P13.2) MUTATED      2   70
  AMP PEAK 43(19P13.2) WILD-TYPE   12  297
                        clus
vv                       AMP PEAK 43(19P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       AMP PEAK 43(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            297
[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    88  27
  AMP PEAK 44(19Q12) WILD-TYPE 369  42
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                         115                          411 
  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                          27                           42 
$`AMP PEAK 44(19Q12) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       41.06        36.69        37.02        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF 
       46.32        14.96         1.18        14.43        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
       18.90         1.64        20.81        10.19        16.87        16.87 
TCGA-AJ-A6NU TCGA-AJ-A8CW TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       20.78         0.13        21.99        63.91        57.80        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX 
       48.79       125.42        36.36        97.71        46.78        36.13 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CR 
       28.54        37.78        16.96        13.55        20.28        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK 
        4.77        71.24        40.80        61.18        19.36         2.96 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN 
       20.52         1.38         0.30         0.30         0.39        80.38 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
       17.85         4.11        75.72        11.87        12.79        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0VT TCGA-BG-A3PP 
       34.13        34.95        22.06        36.49        24.39         6.81 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       10.22        24.13        16.64        67.20        49.55        22.55 
TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1NX 
       39.48        27.42        11.51        18.67         0.72        18.25 
TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
        2.07        16.93         9.37        12.39        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU 
       48.36        10.92        51.52        51.42        19.40        22.26 
TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 
       16.34         6.90        17.62        15.09        15.81        12.59 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX 
       29.10        11.38        17.92        14.70         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       41.06        59.01         9.07        28.93        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06        45.01         7.76        14.04         2.43        23.74 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
        9.47        26.10        23.24        23.97         7.00         4.44 
TCGA-SL-A6J9 
        0.07 

$`AMP PEAK 44(19Q12) WILD-TYPE`
TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
        0.39        19.79        29.39         2.40        34.36         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        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
       22.32        12.82         2.70        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        23.87        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-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        21.90         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-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-A1CP TCGA-AX-A2H4 TCGA-AX-A2HA 
       54.12        67.50        25.12        36.39        30.12        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.26         1.18        18.35        14.47        56.91        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        27.29        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-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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        14.27        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        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-A0VV 
       39.32        30.81        21.17        20.28        15.42        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        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98         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-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-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        13.22        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-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-E6-A1LX TCGA-E6-A1M0 
       39.29        36.62        24.30        35.38        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        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       57.60        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        26.96        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       16.11        12.43        11.08         6.48        19.33        10.19 
TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2D0 
       27.35        13.84        14.14        19.89        16.96        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 
       39.95         7.99        13.84         8.98        96.69        28.96 
TCGA-H5-A2HR TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 
        1.74        13.28        18.21        15.45        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.07        18.28         0.23 

  AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE 
                        0.07                         0.20 
  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 
                       20.52                        23.90 
[1] "0.1 - 125.4 (20.5)" "0.2 - 191.8 (23.9)"
[1] "hr=" "2.6"
D44V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 44(19Q12) MUTATED                                        29
  AMP PEAK 44(19Q12) WILD-TYPE                                     366
                              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                                  77
  AMP PEAK 44(19Q12) WILD-TYPE                                35
D44V3, multiclass
                                         clus
vv                                        AMP PEAK 44(19Q12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         29
  MIXED SEROUS AND ENDOMETRIOID                                   10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               77
                                         clus
vv                                        AMP PEAK 44(19Q12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          366
  MIXED SEROUS AND ENDOMETRIOID                                     11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V4, binary
                              cls
clus                             0   1
  AMP PEAK 44(19Q12) MUTATED    26  90
  AMP PEAK 44(19Q12) WILD-TYPE 115 297
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(19Q12) MUTATED     26   90
  AMP PEAK 44(19Q12) WILD-TYPE  115  297
     clus
vv    AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE
  NO                          26                          115
  YES                         90                          297
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 44(19Q12) MUTATED    74   5   6  11
  AMP PEAK 44(19Q12) WILD-TYPE 289  18  11  24
D44V5, multiclass
    clus
vv   AMP PEAK 44(19Q12) MUTATED AMP PEAK 44(19Q12) WILD-TYPE
  R0                         74                          289
  R1                          5                           18
  R2                          6                           11
  RX                         11                           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 44(19Q12) MUTATED                                  1     2
  AMP PEAK 44(19Q12) WILD-TYPE                                3    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 44(19Q12) MUTATED                          43
  AMP PEAK 44(19Q12) WILD-TYPE                        58
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 44(19Q12) MUTATED                                           3    62
  AMP PEAK 44(19Q12) WILD-TYPE                                         6   304
D44V6, multiclass
                                           clus
vv                                          AMP PEAK 44(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         43
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          3
  WHITE                                                             62
                                           clus
vv                                          AMP PEAK 44(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            6
  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"
D44V7, binary
                              cls
clus                             0   1
  AMP PEAK 44(19Q12) MUTATED     3  82
  AMP PEAK 44(19Q12) WILD-TYPE  11 285
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 44(19Q12) MUTATED      3   82
  AMP PEAK 44(19Q12) WILD-TYPE   11  285
                        clus
vv                       AMP PEAK 44(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         82
                        clus
vv                       AMP PEAK 44(19Q12) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          285
[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    99  17
  AMP PEAK 45(20P13) WILD-TYPE 358  52
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                         116                          410 
  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                          17                           52 
$`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        14.43         2.40        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A05D 
        1.64        22.26        20.81        10.19        16.87        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        46.78        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-A3G6 
       30.12         2.96        64.93        43.82         0.20         0.26 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0KB TCGA-B5-A11I 
        0.30         0.39        80.38        43.13         4.11        75.72 
TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
       45.90        19.56        11.87        12.79       116.25        33.11 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 
       14.27        29.65        34.13        30.81        24.39        52.83 
TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L 
       12.56        15.45         1.81        10.22        10.16        24.13 
TCGA-BK-A4ZD TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 
       16.64        13.18         4.80        67.20        72.72        49.55 
TCGA-D1-A0ZU TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J 
       28.67        22.55         4.44        37.32        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NO 
       31.07        18.67         0.72        41.42         4.11         9.37 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
       48.36        27.32        10.92        37.71        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1G7 
       19.40        34.39        35.15        26.96        22.26         6.21 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A212 
        4.54        23.90         6.90        17.62        15.09        10.19 
TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2EW 
       14.40        29.10        27.35        14.70        40.01        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI 
        9.07        28.93        25.02        29.23        45.01         7.76 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       14.04        23.74         9.47        26.10        23.97        12.92 
TCGA-PG-A915 TCGA-SL-A6J9 
        7.00         0.07 

$`AMP PEAK 45(20P13) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        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-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O 
        9.60         8.02        28.64         5.33         5.16        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
        0.39        19.79        29.39        34.36        34.16         1.12 
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        17.06        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         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-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       117.99       110.37        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-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-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        21.90        36.13         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-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-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-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 
       72.56        54.12        67.50        25.12        36.39        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        20.52         1.38         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        56.91        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        27.29 
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-A11J TCGA-B5-A11N TCGA-B5-A11O 
      185.79       113.36        88.34        54.44        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-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-A3FA TCGA-B5-A3FB 
       14.40        14.70        11.70        15.29        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-A0M8 
       20.94        35.21        34.98        22.06        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-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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 
        6.21        31.76        24.99        10.03         9.86        46.95 
TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD TCGA-BS-A0TG TCGA-BS-A0TI TCGA-BS-A0TJ 
       23.47        85.55        78.21        77.95        61.87        67.99 
TCGA-BS-A0U5 TCGA-BS-A0U7 TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ 
       96.49        30.74        97.41        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-A0ZV TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W 
        4.87        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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1NY 
        2.33        22.92         1.41        13.22        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 
       35.38        12.39        31.10       110.10        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        16.04         7.36        16.80        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AU 
       61.74        61.55        66.90        46.26        57.60        26.43 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        16.34        14.53        24.89 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-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-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX 
       18.87        22.82        20.05        45.76        31.04        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 
       96.69        28.96        41.06         1.74         2.43        13.28 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        23.24        15.45        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       18.28         0.23 

  AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE 
                        0.07                         0.13 
  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 
                      21.535                       23.470 
[1] "0.1 - 125.4 (21.5)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.3"
D45V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 45(20P13) MUTATED                                        52
  AMP PEAK 45(20P13) WILD-TYPE                                     343
                              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                                  59
  AMP PEAK 45(20P13) WILD-TYPE                                53
D45V3, multiclass
                                         clus
vv                                        AMP PEAK 45(20P13) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         52
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               59
                                         clus
vv                                        AMP PEAK 45(20P13) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          343
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                              cls
clus                             0   1
  AMP PEAK 45(20P13) MUTATED    22  94
  AMP PEAK 45(20P13) WILD-TYPE 119 293
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 45(20P13) MUTATED     22   94
  AMP PEAK 45(20P13) WILD-TYPE  119  293
     clus
vv    AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE
  NO                          22                          119
  YES                         94                          293
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 45(20P13) MUTATED    76   4   6   8
  AMP PEAK 45(20P13) WILD-TYPE 287  19  11  27
D45V5, multiclass
    clus
vv   AMP PEAK 45(20P13) MUTATED AMP PEAK 45(20P13) WILD-TYPE
  R0                         76                          287
  R1                          4                           19
  R2                          6                           11
  RX                          8                           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 45(20P13) MUTATED                                  0     4
  AMP PEAK 45(20P13) WILD-TYPE                                4    16
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  AMP PEAK 45(20P13) MUTATED                          33
  AMP PEAK 45(20P13) WILD-TYPE                        68
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 45(20P13) MUTATED                                           2    69
  AMP PEAK 45(20P13) WILD-TYPE                                         7   297
D45V6, multiclass
                                           clus
vv                                          AMP PEAK 45(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              4
  BLACK OR AFRICAN AMERICAN                                         33
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             69
                                           clus
vv                                          AMP PEAK 45(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               16
  BLACK OR AFRICAN AMERICAN                                           68
  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"
D45V7, binary
                              cls
clus                             0   1
  AMP PEAK 45(20P13) MUTATED     1  79
  AMP PEAK 45(20P13) WILD-TYPE  13 288
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 45(20P13) MUTATED      1   79
  AMP PEAK 45(20P13) WILD-TYPE   13  288
                        clus
vv                       AMP PEAK 45(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         79
                        clus
vv                       AMP PEAK 45(20P13) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          288
[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   117  31
  AMP PEAK 46(20Q11.21) WILD-TYPE 340  38
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                            148                             378 
  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                             31                              38 
$`AMP PEAK 46(20Q11.21) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 
       36.69       149.56        37.02        11.44        36.33        46.32 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK 
       28.64         7.33        14.96         1.18        14.43         0.39 
TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 
        2.40        34.16        18.90         1.64        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05D 
       20.81        10.19        16.87        16.87        63.91        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-A1DO TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW 
       31.30        46.78        21.90        53.92        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 
       16.96        20.28        12.43        11.08         4.77        30.12 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       19.36         2.96         0.23         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
       20.52         1.38         0.30         0.26         0.30         0.39 
TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
       80.38        43.13        27.29        17.85         4.11        75.72 
TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
       45.90        19.56       102.31        11.87        12.79       116.25 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
       33.11        14.27        29.65        34.13        34.95        22.06 
TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A18C TCGA-BG-A221 
       36.49        30.81        24.39        52.83        15.45         1.81 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE TCGA-BS-A0U9 
       10.22        10.16        24.13        13.18         4.80        67.20 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A102 TCGA-D1-A169 TCGA-D1-A16I 
       72.72        49.55         8.55         4.44        37.32        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NW 
       29.92        31.07        18.67        14.73        28.08         0.72 
TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
        2.07        41.42         4.11        35.38        12.39       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y 
       48.36        27.32        10.92        49.15        37.71        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       51.42        19.40        35.15        26.96        22.26        16.34 
TCGA-EY-A1G7 TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
        6.21        23.90         6.90        17.62        15.09        11.08 
TCGA-EY-A1GX TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 
        6.48        12.59        14.40        20.05        29.10        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D2 
       13.84        17.92        14.70         5.88        40.01        39.95 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01         9.07        28.93        25.02        41.06        45.01 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 
        7.76        14.04        23.74         9.47        26.10        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       12.92         7.00         4.44         0.07 

$`AMP PEAK 46(20Q11.21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       41.06        10.29       106.88        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL 
        8.02        91.04         5.33         5.16        10.26        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       29.39        34.36         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         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-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
        8.22        23.87        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-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-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-A5FX TCGA-AW-A1PO 
       30.90        10.42        27.85        16.24        36.13         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-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-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE 
       65.88        13.28        19.20        13.55        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-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13        64.93         0.20 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU 
        1.18        18.35        14.47        56.91        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-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-A11N TCGA-B5-A11O 
      185.79       113.36        88.34        54.44        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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        11.70        15.29        96.30        78.81        62.14 
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-A0MT TCGA-BG-A0MU 
       23.47        43.30        43.04        39.32        21.17        20.28 
TCGA-BG-A0RY TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 
       15.42        26.66        16.34        34.29        52.64        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         9.57        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
        6.81        35.90        34.98         6.21        31.76        24.99 
TCGA-BK-A4ZD TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC 
       16.64        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-A0UV 
       97.41        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        62.79        63.58        63.16        66.48        16.83 
TCGA-D1-A0ZO TCGA-D1-A0ZP TCGA-D1-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79        29.95         0.56         4.87        28.67        23.93 
TCGA-D1-A0ZZ TCGA-D1-A101 TCGA-D1-A103 TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X 
       22.55         1.74        21.99        39.48        30.08        29.88 
TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 
        1.91         3.68        29.33        32.58         0.66        15.72 
TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O 
       36.10        36.36        37.51        36.79        27.42        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-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-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-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG 
        3.95         3.52         8.48        44.88         0.26         4.27 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30         9.37        31.10        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        16.04         7.36        16.80        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        34.39        26.43 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 
       17.19        27.16        17.88        14.53        24.89        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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-A1H0 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
       12.43        15.81        19.33        10.19        18.87        22.82 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 
       45.76        31.04        11.38        14.14        19.89        16.96 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       41.06        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W4 
       28.96        29.23         1.74         2.43        13.28        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        15.45        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.83        14.07        18.28         0.23 

  AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE 
                           0.07                            0.13 
  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 
                         20.400                          23.785 
[1] "0.1 - 149.6 (20.4)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2.4"
D46V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 46(20Q11.21) MUTATED                                        62
  AMP PEAK 46(20Q11.21) WILD-TYPE                                     333
                                 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                                  81
  AMP PEAK 46(20Q11.21) WILD-TYPE                                31
D46V3, multiclass
                                         clus
vv                                        AMP PEAK 46(20Q11.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            62
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  81
                                         clus
vv                                        AMP PEAK 46(20Q11.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             333
  MIXED SEROUS AND ENDOMETRIOID                                        15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                                 cls
clus                                0   1
  AMP PEAK 46(20Q11.21) MUTATED    27 122
  AMP PEAK 46(20Q11.21) WILD-TYPE 114 265
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 46(20Q11.21) MUTATED     27  122
  AMP PEAK 46(20Q11.21) WILD-TYPE  114  265
     clus
vv    AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE
  NO                             27                             114
  YES                           122                             265
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 46(20Q11.21) MUTATED    93   5   9  10
  AMP PEAK 46(20Q11.21) WILD-TYPE 270  18   8  25
D46V5, multiclass
    clus
vv   AMP PEAK 46(20Q11.21) MUTATED AMP PEAK 46(20Q11.21) WILD-TYPE
  R0                            93                             270
  R1                             5                              18
  R2                             9                               8
  RX                            10                              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 46(20Q11.21) MUTATED                                  1     5
  AMP PEAK 46(20Q11.21) WILD-TYPE                                3    15
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 46(20Q11.21) MUTATED                          43
  AMP PEAK 46(20Q11.21) WILD-TYPE                        58
                                 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      88
  AMP PEAK 46(20Q11.21) WILD-TYPE   278
D46V6, multiclass
                                           clus
vv                                          AMP PEAK 46(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            43
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                88
                                           clus
vv                                          AMP PEAK 46(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  15
  BLACK OR AFRICAN AMERICAN                                              58
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  WHITE                                                                 278
[1] 5 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  99
  AMP PEAK 46(20Q11.21) WILD-TYPE   9 268
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 46(20Q11.21) MUTATED      5   99
  AMP PEAK 46(20Q11.21) WILD-TYPE    9  268
                        clus
vv                       AMP PEAK 46(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            99
                        clus
vv                       AMP PEAK 46(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             268
[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   120  28
  AMP PEAK 47(20Q13.12) WILD-TYPE 337  41
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                            148                             378 
  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                             28                              41 
$`AMP PEAK 47(20Q13.12) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A1OH 
       41.06        36.69       149.56        19.96        11.44        36.33 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       91.04        46.32        28.64         7.33         1.18        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        0.39         2.40        34.16        18.90         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05A 
       20.81        10.19        16.87        16.87         5.95        63.91 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A3K1 
      125.42         3.39        97.71        31.30        46.78        21.90 
TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       53.92        28.54        37.78        16.96        13.55        20.28 
TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HK 
       12.43        11.08         4.77        30.12        71.24         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.23        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0K8 
        0.26         0.30         0.39        80.38        43.13        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MR TCGA-B5-A1MS 
        4.11        75.72        45.90        19.56       191.84       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FB TCGA-B5-A3FD TCGA-B5-A3S1 
       11.87        12.79       116.25        78.81        33.11        29.65 
TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YV 
       34.95        36.49        30.81        24.39        52.83        12.56 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE 
       15.45         1.81        10.22        24.13        13.18         4.80 
TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A102 
       67.20        72.72        49.55        29.95         8.55         4.44 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
       37.32        11.51        29.92        31.07        18.67         3.95 
TCGA-D1-A176 TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 
       30.15        14.73        28.08         0.72        18.25         2.07 
TCGA-D1-A2G5 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
       41.42         4.11        35.38        12.39       110.10        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
       27.32        10.92        49.15        37.71        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1G7 
       19.40        35.15        26.96        22.26        16.34         6.21 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A1GX 
       23.90         6.90        17.62        15.09        11.08         6.48 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       12.59        14.40        20.05        29.10        27.35        11.38 
TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D2 
       17.92        14.70         5.88        40.01        41.06        39.95 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01         9.07        25.02        29.23        41.06        45.01 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A7D5 
        7.76        14.04        23.74         9.47        26.10        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       12.92         7.00         4.44         0.07 

$`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 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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        10.26        19.79        29.39 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36         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 
       17.06        36.99        20.65        21.21        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-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-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       48.79       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-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-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       16.24        36.13         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-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-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-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12        36.39        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       64.93         0.20         0.56         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        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        27.29        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-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3FA TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       96.30        62.14        14.27        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        22.06 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        39.32        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        56.58        14.83 
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 
       20.02        23.70        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-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-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-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A177 TCGA-D1-A17A 
        3.65        17.49        19.53         6.64        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
       22.92         1.41        13.22        16.87        18.02        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        1.05         3.95         3.52         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        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        16.04         7.36        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS 
       61.74        61.55        66.90        46.26        57.60        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 
       26.43        17.19        27.16        17.88        14.53        24.89 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.34        22.78        13.97        19.27        18.84        17.88 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 
       16.11        12.43        15.81        19.33        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 
       22.82        45.76        31.04        13.84        14.14        19.89 
TCGA-EY-A5W2 TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       16.96        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W4 
       28.93        28.96         1.74         2.43        13.28        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        15.45        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.83        14.07        18.28         0.23 

  AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE 
                           0.07                            0.13 
  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 
                          20.40                           23.67 
[1] "0.1 - 191.8 (20.4)" "0.1 - 185.8 (23.7)"
[1] "hr=" "1.9"
D47V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 47(20Q13.12) MUTATED                                        64
  AMP PEAK 47(20Q13.12) WILD-TYPE                                     331
                                 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                                  78
  AMP PEAK 47(20Q13.12) WILD-TYPE                                34
D47V3, multiclass
                                         clus
vv                                        AMP PEAK 47(20Q13.12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            64
  MIXED SEROUS AND ENDOMETRIOID                                       7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  78
                                         clus
vv                                        AMP PEAK 47(20Q13.12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             331
  MIXED SEROUS AND ENDOMETRIOID                                        14
  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"
D47V4, binary
                                 cls
clus                                0   1
  AMP PEAK 47(20Q13.12) MUTATED    25 124
  AMP PEAK 47(20Q13.12) WILD-TYPE 116 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 47(20Q13.12) MUTATED     25  124
  AMP PEAK 47(20Q13.12) WILD-TYPE  116  263
     clus
vv    AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE
  NO                             25                             116
  YES                           124                             263
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 47(20Q13.12) MUTATED    91   7   9  12
  AMP PEAK 47(20Q13.12) WILD-TYPE 272  16   8  23
D47V5, multiclass
    clus
vv   AMP PEAK 47(20Q13.12) MUTATED AMP PEAK 47(20Q13.12) WILD-TYPE
  R0                            91                             272
  R1                             7                              16
  R2                             9                               8
  RX                            12                              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 47(20Q13.12) MUTATED                                  1     5
  AMP PEAK 47(20Q13.12) WILD-TYPE                                3    15
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 47(20Q13.12) MUTATED                          43
  AMP PEAK 47(20Q13.12) WILD-TYPE                        58
                                 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      87
  AMP PEAK 47(20Q13.12) WILD-TYPE   279
D47V6, multiclass
                                           clus
vv                                          AMP PEAK 47(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 5
  BLACK OR AFRICAN AMERICAN                                            43
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                87
                                           clus
vv                                          AMP PEAK 47(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  15
  BLACK OR AFRICAN AMERICAN                                              58
  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"
D47V7, binary
                                 cls
clus                                0   1
  AMP PEAK 47(20Q13.12) MUTATED     5 104
  AMP PEAK 47(20Q13.12) WILD-TYPE   9 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 47(20Q13.12) MUTATED      5  104
  AMP PEAK 47(20Q13.12) WILD-TYPE    9  263
                        clus
vv                       AMP PEAK 47(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           104
                        clus
vv                       AMP PEAK 47(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             263
[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   121  28
  AMP PEAK 48(20Q13.33) WILD-TYPE 336  41
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                            149                             377 
  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                             28                              41 
$`AMP PEAK 48(20Q13.33) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A1OG 
       41.06        36.69       149.56        37.02        65.75        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       36.33        91.04        46.32        28.64         7.33        14.96 
TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF 
        1.18        14.43         0.39         2.40        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS 
       18.90         1.64        22.26        20.81        10.19        16.87 
TCGA-AJ-A3TW TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A0LF 
       16.87        63.91        57.80        45.53       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        46.78        21.90        53.92        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF 
       37.78        16.96        13.55        20.28        12.43        76.83 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A2HK 
       11.08         4.77        30.12        71.24        19.36         2.96 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.23        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JT TCGA-B5-A0JX 
        0.26         0.30         0.39        80.38        43.13        44.71 
TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11L TCGA-B5-A11V TCGA-B5-A1MR 
       17.85         4.11        75.72        45.90        19.56       191.84 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 
      102.31        11.87       116.25        33.11        14.27        29.65 
TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0MS TCGA-BG-A0VT TCGA-BG-A0W1 TCGA-BG-A0YV 
       34.95        36.49        30.81        24.39        52.83        12.56 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A56F TCGA-BS-A0TE 
       15.45         1.81        10.22        24.13        13.18         4.80 
TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ 
       61.87        67.20        72.72        49.55         8.55        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-A16V TCGA-D1-A17K TCGA-D1-A1NW TCGA-D1-A1O0 TCGA-D1-A2G5 TCGA-D1-A3DH 
        3.95        28.08         0.72         2.07        41.42         4.11 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A1LZ 
       16.93        35.38         9.37        12.39       110.10        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22Y TCGA-EO-A2CG 
       27.32        10.92        49.15        37.71        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GC 
       19.40        35.15        17.88        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        11.08         6.48        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       10.19        14.40        20.05        29.10        27.35        11.38 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F9 
       14.70         5.88        40.01        59.01         9.07        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 
       41.06        45.01         7.76        23.74         9.47        26.10 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.97        12.92         7.00         4.44         0.07 

$`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 
       10.29       106.88        83.51        17.85        32.78       112.54 
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        10.26        19.79        29.39        34.36         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        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         2.70         0.13        83.67        21.99 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N 
        5.95        23.31        86.07         8.22        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       12.20        20.91        48.79       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-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       60.36        55.89        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         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-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-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.28        19.20        15.25        20.05        72.56        54.12 
TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       67.50        25.12        36.39        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       64.93         0.20         0.56         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       56.91        46.75        48.76        40.67        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        27.29        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-A1N2 
       50.89        14.40        14.70        11.70        15.29        12.79 
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-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
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-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        43.04        39.32        21.17        20.28        15.42 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        56.58        14.83 
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 
       20.02        23.70        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-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-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-A101 TCGA-D1-A103 
        0.56         4.87        28.67        23.93         1.74        21.99 
TCGA-D1-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       39.48        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       36.79        27.42        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        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-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-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       44.88         0.26         4.27        89.33        10.92        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        16.04         7.36        16.80 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A3AS 
       61.74        61.55        66.90        46.26        57.60        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX 
       26.43        17.19        27.16        26.96        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       24.89        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.90        22.78        13.97        19.27        18.84 
TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1H0 TCGA-EY-A215 
       17.88        16.11        12.43        15.81        19.33        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       22.82        45.76        31.04        13.84        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       19.89        16.96        41.06        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        96.69        28.93        28.96        25.02 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC 
        1.74        14.04         2.43        13.28        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.23 

  AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE 
                           0.07                            0.13 
  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 
                          20.28                           23.87 
[1] "0.1 - 191.8 (20.3)" "0.1 - 185.8 (23.9)"
[1] "hr=" "1.8"
D48V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 48(20Q13.33) MUTATED                                        67
  AMP PEAK 48(20Q13.33) WILD-TYPE                                     328
                                 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                                  77
  AMP PEAK 48(20Q13.33) WILD-TYPE                                35
D48V3, multiclass
                                         clus
vv                                        AMP PEAK 48(20Q13.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            67
  MIXED SEROUS AND ENDOMETRIOID                                       6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  77
                                         clus
vv                                        AMP PEAK 48(20Q13.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             328
  MIXED SEROUS AND ENDOMETRIOID                                        15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                                 cls
clus                                0   1
  AMP PEAK 48(20Q13.33) MUTATED    25 125
  AMP PEAK 48(20Q13.33) WILD-TYPE 116 262
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 48(20Q13.33) MUTATED     25  125
  AMP PEAK 48(20Q13.33) WILD-TYPE  116  262
     clus
vv    AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE
  NO                             25                             116
  YES                           125                             262
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 48(20Q13.33) MUTATED    91   7  10  13
  AMP PEAK 48(20Q13.33) WILD-TYPE 272  16   7  22
D48V5, multiclass
    clus
vv   AMP PEAK 48(20Q13.33) MUTATED AMP PEAK 48(20Q13.33) WILD-TYPE
  R0                            91                             272
  R1                             7                              16
  R2                            10                               7
  RX                            13                              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 48(20Q13.33) MUTATED                                  1     6
  AMP PEAK 48(20Q13.33) WILD-TYPE                                3    14
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  AMP PEAK 48(20Q13.33) MUTATED                          41
  AMP PEAK 48(20Q13.33) WILD-TYPE                        60
                                 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      92
  AMP PEAK 48(20Q13.33) WILD-TYPE   274
D48V6, multiclass
                                           clus
vv                                          AMP PEAK 48(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 6
  BLACK OR AFRICAN AMERICAN                                            41
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                92
                                           clus
vv                                          AMP PEAK 48(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  14
  BLACK OR AFRICAN AMERICAN                                              60
  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"
D48V7, binary
                                 cls
clus                                0   1
  AMP PEAK 48(20Q13.33) MUTATED     4 105
  AMP PEAK 48(20Q13.33) WILD-TYPE  10 262
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 48(20Q13.33) MUTATED      4  105
  AMP PEAK 48(20Q13.33) WILD-TYPE   10  262
                        clus
vv                       AMP PEAK 48(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           105
                        clus
vv                       AMP PEAK 48(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                  10
  NOT HISPANIC OR LATINO                             262
[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    44  17
  AMP PEAK 49(22Q12.2) WILD-TYPE 413  52
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            61                            465 
  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                            17                             52 
$`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        29.39        34.16        63.91 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AX-A1C8 TCGA-AX-A1CF 
      125.42         3.39        97.71        21.90        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         0.39        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        29.65        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        14.73        13.22         0.72 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CH 
       16.93        35.38        27.32        10.92        37.71        19.40 
TCGA-EO-A3AS TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A2ON 
       34.39        23.90        19.27        15.09        10.19        20.05 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2CY 
       27.35        13.84        11.38        14.70        40.01        41.06 
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-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       14.04         9.47        18.21        23.97        12.92         7.00 
TCGA-QS-A8F1 
        4.44 

$`AMP PEAK 49(22Q12.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N 
       46.32         5.33         5.16         7.33        14.96        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26         0.39        19.79         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         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-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ 
       48.79       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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         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-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-A2H7 
       67.50        25.12        36.39        11.08        30.12        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       17.75        30.74         2.96        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-B5-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-A0KB 
       27.29        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-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-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MY TCGA-B5-A1MZ 
       16.57        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-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        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        22.06        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-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-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-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        1.41        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27         4.11        89.33        10.92        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-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        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-A22R 
        6.67        16.04         7.36        16.80        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
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        11.08         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-A2OQ TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       29.10        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 
       39.88        39.95         7.99        13.84         8.98        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       29.23        45.01         1.74         7.76         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       13.28        26.10        23.24        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE 
                          0.39                           0.07 
  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 
                         21.90                          23.34 
[1] "0.4 - 191.8 (21.9)" "0.1 - 185.8 (23.3)"
[1] "hr=" "2.6"
D49V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 49(22Q12.2) MUTATED                                        11
  AMP PEAK 49(22Q12.2) WILD-TYPE                                     384
                                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                                  49
  AMP PEAK 49(22Q12.2) WILD-TYPE                                63
D49V3, multiclass
                                         clus
vv                                        AMP PEAK 49(22Q12.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           11
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 49
                                         clus
vv                                        AMP PEAK 49(22Q12.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            384
  MIXED SEROUS AND ENDOMETRIOID                                       19
  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"
D49V4, binary
                                cls
clus                               0   1
  AMP PEAK 49(22Q12.2) MUTATED    10  52
  AMP PEAK 49(22Q12.2) WILD-TYPE 131 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(22Q12.2) MUTATED     10   52
  AMP PEAK 49(22Q12.2) WILD-TYPE  131  335
     clus
vv    AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE
  NO                            10                            131
  YES                           52                            335
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 49(22Q12.2) MUTATED    35   3   7   6
  AMP PEAK 49(22Q12.2) WILD-TYPE 328  20  10  29
D49V5, multiclass
    clus
vv   AMP PEAK 49(22Q12.2) MUTATED AMP PEAK 49(22Q12.2) WILD-TYPE
  R0                           35                            328
  R1                            3                             20
  R2                            7                             10
  RX                            6                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 49(22Q12.2) MUTATED                                  0     1
  AMP PEAK 49(22Q12.2) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 49(22Q12.2) MUTATED                          21
  AMP PEAK 49(22Q12.2) WILD-TYPE                        80
                                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      34
  AMP PEAK 49(22Q12.2) WILD-TYPE   332
D49V6, multiclass
                                           clus
vv                                          AMP PEAK 49(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               34
                                           clus
vv                                          AMP PEAK 49(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             80
  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"
D49V7, binary
                                cls
clus                               0   1
  AMP PEAK 49(22Q12.2) MUTATED     2  43
  AMP PEAK 49(22Q12.2) WILD-TYPE  12 324
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 49(22Q12.2) MUTATED      2   43
  AMP PEAK 49(22Q12.2) WILD-TYPE   12  324
                        clus
vv                       AMP PEAK 49(22Q12.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           43
                        clus
vv                       AMP PEAK 49(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            324
[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    73  16
  AMP PEAK 50(XP11.23) WILD-TYPE 384  53
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            89                            437 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                            16                             53 
$`AMP PEAK 50(XP11.23) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GV TCGA-A5-A2K2 TCGA-AJ-A3BD TCGA-AJ-A3EM 
       36.69        65.75        20.81        91.04        34.16        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NG TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A8CW TCGA-AP-A05D 
       20.81        15.62        16.87        16.87         0.13        57.80 
TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AX-A05W 
        3.39        33.40        31.30        46.78        16.24        68.35 
TCGA-AX-A0IW TCGA-AX-A1CC TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       37.78        12.43        11.08        30.12        40.80        81.37 
TCGA-AX-A2HH TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K4 
       17.75         0.39        56.91        43.13        27.29        17.88 
TCGA-B5-A11R TCGA-B5-A11S TCGA-B5-A1MU TCGA-B5-A5OD TCGA-BG-A0M0 TCGA-BG-A0M2 
       33.50        27.35        50.89        34.13        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV 
       35.21        34.98        30.81        15.42        52.83        12.56 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        10.22        10.16        24.13         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A102 TCGA-D1-A165 
       72.72        49.55        29.95        22.55         4.44         0.66 
TCGA-D1-A168 TCGA-D1-A17R TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-DI-A2QY 
       36.10        11.15        41.42         8.48         4.11       110.10 
TCGA-E6-A1M0 TCGA-EO-A1Y5 TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EO-A3KU 
       17.06        10.92        51.52        34.39        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       16.34         6.21        23.34        17.88        17.62        15.09 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-FI-A2CY 
        6.48        19.33        10.19        29.10        27.35        41.06 
TCGA-FI-A2D4 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KP-A3VZ 
        7.99        59.01         9.07        41.06        14.04        23.74 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SL-A6J9 
        9.47        26.10        14.83         4.44         0.07 

$`AMP PEAK 50(XP11.23) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        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-A2K3 TCGA-A5-A2K4 TCGA-A5-A2K5 
       36.33         9.60         8.02        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        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
        0.39        19.79        29.39         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       17.06        36.99        20.65        21.21        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-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-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       63.91        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       48.79       125.42       117.99       110.37        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-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-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       27.85        21.90        36.13         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-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-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-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HD 
       36.39         4.77        71.24        61.18        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47        80.38        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-A0K6 
       32.55        28.64        28.34        30.51        25.91        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-A11U TCGA-B5-A11V TCGA-B5-A11W 
       40.50        36.82        32.09        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-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M6 TCGA-BG-A0M7 
       41.06        34.95        18.61        20.19        22.06        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-A0MT TCGA-BG-A0MU TCGA-BG-A0VT 
       43.30        43.04        39.32        21.17        20.28        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
        6.81        34.98         6.21        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-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-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-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-A169 TCGA-D1-A16B 
        3.68        29.33        32.58        15.72        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S 
       28.08        26.37        10.22         1.51         1.78        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
        3.52        44.88         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       35.38         9.37        12.39        31.10        23.38        48.36 
TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G 
        2.37         6.67        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.42        19.40        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC 
       27.16        17.88        14.53        24.89        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK 
       53.88        24.36        27.16        23.34        23.90        22.78 
TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        19.27        18.84        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81        11.08        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-A547 
       20.05        45.76        31.04        13.84        11.38        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY 
       39.88        39.95        13.84         8.98        96.69        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.96        25.02        29.23        45.01         1.74         7.76 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
        2.43        13.28        18.21        23.24        15.45        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 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.07        18.28         0.23 

  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                          0.07                           0.20 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                        110.10                         191.84 
  AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE 
                         22.55                          23.38 
[1] "0.1 - 110.1 (22.6)" "0.2 - 191.8 (23.4)"
[1] "hr=" "1.6"
D50V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 50(XP11.23) MUTATED                                        52
  AMP PEAK 50(XP11.23) WILD-TYPE                                     343
                                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                                  33
  AMP PEAK 50(XP11.23) WILD-TYPE                                79
D50V3, multiclass
                                         clus
vv                                        AMP PEAK 50(XP11.23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           52
  MIXED SEROUS AND ENDOMETRIOID                                      4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 33
                                         clus
vv                                        AMP PEAK 50(XP11.23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            343
  MIXED SEROUS AND ENDOMETRIOID                                       17
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                                cls
clus                               0   1
  AMP PEAK 50(XP11.23) MUTATED    15  74
  AMP PEAK 50(XP11.23) WILD-TYPE 126 313
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(XP11.23) MUTATED     15   74
  AMP PEAK 50(XP11.23) WILD-TYPE  126  313
     clus
vv    AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE
  NO                            15                            126
  YES                           74                            313
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 50(XP11.23) MUTATED    61   3   5   7
  AMP PEAK 50(XP11.23) WILD-TYPE 302  20  12  28
D50V5, multiclass
    clus
vv   AMP PEAK 50(XP11.23) MUTATED AMP PEAK 50(XP11.23) WILD-TYPE
  R0                           61                            302
  R1                            3                             20
  R2                            5                             12
  RX                            7                             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 50(XP11.23) MUTATED                                  0     2
  AMP PEAK 50(XP11.23) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  AMP PEAK 50(XP11.23) MUTATED                          18
  AMP PEAK 50(XP11.23) WILD-TYPE                        83
                                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      61
  AMP PEAK 50(XP11.23) WILD-TYPE   305
D50V6, multiclass
                                           clus
vv                                          AMP PEAK 50(XP11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               61
                                           clus
vv                                          AMP PEAK 50(XP11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             83
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                305
[1] 5 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  67
  AMP PEAK 50(XP11.23) WILD-TYPE  13 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 50(XP11.23) MUTATED      1   67
  AMP PEAK 50(XP11.23) WILD-TYPE   13  300
                        clus
vv                       AMP PEAK 50(XP11.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK 50(XP11.23) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            300
[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    67  21
  AMP PEAK 51(XQ28) WILD-TYPE 390  48
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         88                         438 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                         21                          48 
$`AMP PEAK 51(XQ28) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GV TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BF TCGA-AJ-A3NG 
       36.69        20.81        14.96        14.43         1.12        15.62 
TCGA-AJ-A8CW TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
        0.13         5.95        63.91        45.53        36.89        48.79 
TCGA-AP-A0LO TCGA-AP-A1DO TCGA-AP-A1DQ TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AX-A05W 
       33.40        31.30        46.78        16.24        36.13        68.35 
TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HH TCGA-AX-A3G3 
        4.77        30.12        40.80        81.37        17.75         1.38 
TCGA-AX-A3G4 TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A11R 
        0.30        80.38        56.91        43.13        27.29        33.50 
TCGA-B5-A11S TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       27.35        11.87        29.65        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0MS TCGA-BG-A0RY TCGA-BG-A0W1 TCGA-BG-A0YV 
       34.98        22.06        30.81        15.42        52.83        12.56 
TCGA-BK-A0C9 TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       35.90        10.22        24.13        16.64         4.80        61.87 
TCGA-BS-A0UT TCGA-BS-A0V8 TCGA-D1-A102 TCGA-D1-A165 TCGA-D1-A168 TCGA-D1-A16R 
       72.72        49.55         4.44         0.66        36.10         0.69 
TCGA-D1-A17R TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A2QT 
       11.15        41.42         8.48         4.11        16.93        12.39 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A22Y 
      110.10        48.36        17.06        27.32        37.71        51.52 
TCGA-EO-A2CH TCGA-EO-A3AV TCGA-EO-A3KU TCGA-EY-A1G7 TCGA-EY-A1GH TCGA-EY-A1GQ 
       19.40        35.15        22.26         6.21        23.34        17.88 
TCGA-EY-A1GR TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A547 
       17.62         6.48        19.33        14.40        27.35        17.92 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-KJ-A3U4 
        5.88        41.06         7.99        29.23        45.01         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-QS-A744 TCGA-QS-A8F1 
       23.74         9.47        14.83         4.44 

$`AMP PEAK 51(XQ28) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.82        28.27        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-A23M TCGA-AJ-A23O 
       28.64         5.33         5.16         7.33         1.18        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       10.19        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AP-A051 TCGA-AP-A052 
       22.32        12.82        20.78         2.70        83.67        21.99 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05D TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        57.80        23.87        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-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-A1DP TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       60.36        55.89        35.54        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       10.42        27.85        21.90         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-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-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-A1CR TCGA-AX-A2H5 TCGA-AX-A2H8 
       67.50        25.12        36.39        11.08        71.24        61.18 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        19.36        26.33        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       14.47         0.39        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-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-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-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-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M7 
       41.06        34.13        34.95        18.61        20.19        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-A0MT TCGA-BG-A0MU TCGA-BG-A0VT 
       43.30        43.04        39.32        21.17        20.28        24.39 
TCGA-BG-A0VV TCGA-BG-A0VW TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W2 TCGA-BG-A0YU 
       26.66        16.34        34.29        52.64        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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
        6.81        34.98         6.21        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-A0UV 
       67.20        88.34        85.84        82.39        81.57        73.25 
TCGA-BS-A0V4 TCGA-BS-A0V6 TCGA-BS-A0V7 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        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-A103 TCGA-D1-A15V TCGA-D1-A15W 
       23.93        22.55         1.74        21.99        39.48        30.08 
TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A167 
       29.88         1.91         3.68        29.33        32.58        15.72 
TCGA-D1-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-A16S TCGA-D1-A16V 
       29.92        31.07        33.63        10.65        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV 
        3.95         3.52        44.88         0.26         4.27        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-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 
       16.04         7.36        16.80        10.92        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        51.42        34.39 
TCGA-EO-A3AU TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       26.43        17.19        27.16        17.88        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89        14.99         4.54        53.88        24.36 
TCGA-EY-A1GF TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM 
       27.16        23.34        23.90        22.78        13.97         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
       19.27        18.84        15.09        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON 
       11.08        12.59        10.19        18.87        22.82        20.05 
TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A548 
       45.76        31.04        29.10        13.84        11.38        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
       19.89        14.70        16.96        40.01        39.88        39.95 
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-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       28.96        25.02        41.06         1.74         7.76        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       13.28        26.10        18.21        23.24        15.45        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 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       12.92        23.64        14.07        18.28         0.07         0.23 

  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                       0.13                        0.07 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                     110.10                      191.84 
  AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE 
                     22.160                      23.425 
[1] "0.1 - 110.1 (22.2)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.4"
D51V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  AMP PEAK 51(XQ28) MUTATED                                        53
  AMP PEAK 51(XQ28) WILD-TYPE                                     342
                             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                                  33
  AMP PEAK 51(XQ28) WILD-TYPE                                79
D51V3, multiclass
                                         clus
vv                                        AMP PEAK 51(XQ28) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        53
  MIXED SEROUS AND ENDOMETRIOID                                   3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              33
                                         clus
vv                                        AMP PEAK 51(XQ28) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         342
  MIXED SEROUS AND ENDOMETRIOID                                    18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                             cls
clus                            0   1
  AMP PEAK 51(XQ28) MUTATED    23  66
  AMP PEAK 51(XQ28) WILD-TYPE 118 321
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 51(XQ28) MUTATED     23   66
  AMP PEAK 51(XQ28) WILD-TYPE  118  321
     clus
vv    AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE
  NO                         23                         118
  YES                        66                         321
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 51(XQ28) MUTATED    63   2   6   6
  AMP PEAK 51(XQ28) WILD-TYPE 300  21  11  29
D51V5, multiclass
    clus
vv   AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE
  R0                        63                         300
  R1                         2                          21
  R2                         6                          11
  RX                         6                          29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 51(XQ28) MUTATED                                  1     2
  AMP PEAK 51(XQ28) WILD-TYPE                                3    18
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  AMP PEAK 51(XQ28) MUTATED                          21
  AMP PEAK 51(XQ28) WILD-TYPE                        80
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  AMP PEAK 51(XQ28) MUTATED                                           2    58
  AMP PEAK 51(XQ28) WILD-TYPE                                         7   308
D51V6, multiclass
                                           clus
vv                                          AMP PEAK 51(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             2
  BLACK OR AFRICAN AMERICAN                                        21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            58
                                           clus
vv                                          AMP PEAK 51(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                          80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  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"
D51V7, binary
                             cls
clus                            0   1
  AMP PEAK 51(XQ28) MUTATED     3  61
  AMP PEAK 51(XQ28) WILD-TYPE  11 306
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 51(XQ28) MUTATED      3   61
  AMP PEAK 51(XQ28) WILD-TYPE   11  306
                        clus
vv                       AMP PEAK 51(XQ28) MUTATED AMP PEAK 51(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             3                          11
  NOT HISPANIC OR LATINO                        61                         306
[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    56  13
  DEL PEAK  1(1P36.21) WILD-TYPE 401  56
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            69                            457 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            13                             56 
$`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 
       10.26         0.39        34.16        10.19        16.87        20.78 
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        43.82        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        14.73 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A2QT TCGA-DI-A2QY 
        2.07        44.88         4.27        16.93        12.39       110.10 
TCGA-EO-A1Y8 TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO 
       37.71        34.39        27.16        16.34         6.90        19.27 
TCGA-EY-A1GP TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A4KR TCGA-EY-A72D 
       18.84        12.59        14.40        45.76        11.38         5.88 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3VZ 
       25.02        29.23        45.01         1.74         7.76        23.74 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 
       26.10        18.21        23.97 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        36.69        10.29       106.88        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        28.64         5.33         5.16 
TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        7.33        14.96        14.43        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36         1.12         0.76        18.90         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        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87        22.32        12.82         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        63.91 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        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 
       46.78        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        21.90        36.13        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-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        16.96        15.25        12.43        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 
       72.56        54.12        67.50        30.12        71.24        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56         0.20        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       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        27.29        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-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       35.21        34.98        22.06        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-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        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       11.31         6.81        35.90        34.98         6.21        10.22 
TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BK-A56F 
       10.16        31.76        24.99        24.13        16.64        13.18 
TCGA-BK-A6W3 TCGA-BK-A6W4 TCGA-BS-A0T9 TCGA-BS-A0TA TCGA-BS-A0TC TCGA-BS-A0TD 
       10.03         9.86        46.95        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-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-A168 TCGA-D1-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       37.51        36.79        27.42        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH 
        3.95         3.52        41.42         8.48         0.26         4.11 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       24.30        35.38         9.37        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        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX 
       35.15        17.19        17.88        26.96        22.26        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        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-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-A212 TCGA-EY-A215 TCGA-EY-A2OM 
       11.08         6.48        19.33        10.19        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       20.05        31.04        29.10        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       14.14        19.89        14.70        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-K6-A3WQ 
       59.01         9.07        28.93        28.96        41.06        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 
        2.43        13.28         9.47        23.24        15.45        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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          0.39                           0.07 
  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 
                         23.97                          23.31 
[1] "0.4 - 149.6 (24.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.5"
D52V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  1(1P36.21) MUTATED                                        26
  DEL PEAK  1(1P36.21) WILD-TYPE                                     369
                                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                                  38
  DEL PEAK  1(1P36.21) WILD-TYPE                                74
D52V3, multiclass
                                         clus
vv                                        DEL PEAK  1(1P36.21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           26
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        DEL PEAK  1(1P36.21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            369
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.21) MUTATED    19  50
  DEL PEAK  1(1P36.21) WILD-TYPE 122 337
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     19   50
  DEL PEAK  1(1P36.21) WILD-TYPE  122  337
     clus
vv    DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  NO                            19                            122
  YES                           50                            337
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.21) MUTATED    50   5   2   3
  DEL PEAK  1(1P36.21) WILD-TYPE 313  18  15  32
D52V5, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  R0                           50                            313
  R1                            5                             18
  R2                            2                             15
  RX                            3                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.21) MUTATED                                  1     1
  DEL PEAK  1(1P36.21) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  1(1P36.21) MUTATED                          19
  DEL PEAK  1(1P36.21) WILD-TYPE                        82
                                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      43
  DEL PEAK  1(1P36.21) WILD-TYPE   323
D52V6, multiclass
                                           clus
vv                                          DEL PEAK  1(1P36.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               43
                                           clus
vv                                          DEL PEAK  1(1P36.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             82
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                323
[1] 5 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  45
  DEL PEAK  1(1P36.21) WILD-TYPE  11 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED      3   45
  DEL PEAK  1(1P36.21) WILD-TYPE   11  322
                        clus
vv                       DEL PEAK  1(1P36.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           45
                        clus
vv                       DEL PEAK  1(1P36.21) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            322
[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  17
  DEL PEAK  2(1P36.11) WILD-TYPE 396  52
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            78                            448 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            17                             52 
$`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 
       10.26         0.39        34.16        20.81        10.19        16.87 
TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LI 
       16.87        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        43.82 
TCGA-AX-A3G3 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
        1.38        75.72        36.82        11.87        12.79        29.65 
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         3.95        14.73        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        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       14.40        20.05        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 
       11.38        28.93        25.02        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 
        7.76        14.04        23.74        26.10        18.21        23.97 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A2K5 
       11.44         9.60         8.02        91.04        28.64         5.33 
TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
        5.16         7.33        14.43        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36         1.12         0.76        18.90         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        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       21.21        15.62        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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-A05N 
        5.95        23.31        86.07         8.22        63.91        23.87 
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        46.78 
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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        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-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-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       19.20        15.25        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        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        19.36        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ 
       31.13        64.93         0.23         0.20         0.56         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.39        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        27.29        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-A11J TCGA-B5-A11L TCGA-B5-A11N TCGA-B5-A11O TCGA-B5-A11Q 
       88.34        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-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-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW 
       62.14        33.11        14.27        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        22.06 
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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         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-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-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-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-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-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-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.11        16.93        89.33        10.92        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 
      110.10        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-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.42        19.40        26.43        35.15        17.19        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       26.96        22.26        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS 
       23.90        22.78        13.97        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        11.08         6.48        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       18.87        22.82        31.04        17.92        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.95         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 
        9.07        28.96        29.23         2.43        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       23.24        15.45        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 
       18.84        39.95        12.92        23.64        14.83         4.44 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                          0.39                           0.07 
  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 
                        20.545                         23.360 
[1] "0.4 - 149.6 (20.5)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.1"
D53V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                                        25
  DEL PEAK  2(1P36.11) WILD-TYPE                                     370
                                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                                  49
  DEL PEAK  2(1P36.11) WILD-TYPE                                63
D53V3, multiclass
                                         clus
vv                                        DEL PEAK  2(1P36.11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           25
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 49
                                         clus
vv                                        DEL PEAK  2(1P36.11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            370
  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"
D53V4, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED    18  61
  DEL PEAK  2(1P36.11) WILD-TYPE 123 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED     18   61
  DEL PEAK  2(1P36.11) WILD-TYPE  123  326
     clus
vv    DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  NO                            18                            123
  YES                           61                            326
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  2(1P36.11) MUTATED    52   7   5   3
  DEL PEAK  2(1P36.11) WILD-TYPE 311  16  12  32
D53V5, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                           52                            311
  R1                            7                             16
  R2                            5                             12
  RX                            3                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P36.11) MUTATED                                  1     1
  DEL PEAK  2(1P36.11) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  2(1P36.11) MUTATED                          20
  DEL PEAK  2(1P36.11) WILD-TYPE                        81
                                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      52
  DEL PEAK  2(1P36.11) WILD-TYPE   314
D53V6, multiclass
                                           clus
vv                                          DEL PEAK  2(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           20
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               52
                                           clus
vv                                          DEL PEAK  2(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             81
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK  2(1P36.11) MUTATED     4  55
  DEL PEAK  2(1P36.11) WILD-TYPE  10 312
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      4   55
  DEL PEAK  2(1P36.11) WILD-TYPE   10  312
                        clus
vv                       DEL PEAK  2(1P36.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK  2(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            312
[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    19   6
  DEL PEAK  3(2P25.3) WILD-TYPE 438  63
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           25                           501 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                            6                            63 
$`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        18.90        22.26        20.81       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        43.82         1.38 
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        20.05        28.93         1.74        23.24 
TCGA-PG-A914 
       12.92 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
        7.92        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 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16         1.12         0.76         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        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         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 
       63.91        57.80        45.53        36.89        23.87        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        46.78 
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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        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-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-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       11.08         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        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        27.29        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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       14.27        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
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        20.02        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-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-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-A16S 
       27.42        29.92        31.07        33.63        10.65        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-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-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-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        0.26         4.27         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        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        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU 
       57.60        51.52        51.42        19.40        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-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-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        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 
       11.38        17.92        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        41.06        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 
       13.84         8.98        96.69        59.01         9.07        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        29.23        41.06        45.01         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
        2.43        23.74        13.28         9.47        26.10        18.21 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       15.45        23.97         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       39.95        12.92        23.64        14.83         4.44        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         18.9                          23.7 
[1] "0.6 - 125.4 (18.9)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.3"
D54V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                        13
  DEL PEAK  3(2P25.3) WILD-TYPE                                     382
                               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                               101
D54V3, multiclass
                                         clus
vv                                        DEL PEAK  3(2P25.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          13
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                11
                                         clus
vv                                        DEL PEAK  3(2P25.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           382
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 101
[1] 3 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  23
  DEL PEAK  3(2P25.3) WILD-TYPE 138 364
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      3   23
  DEL PEAK  3(2P25.3) WILD-TYPE  138  364
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                            3                           138
  YES                          23                           364
[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 346  23  15  33
D54V5, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          17                           346
  R1                           0                            23
  R2                           2                            15
  RX                           2                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2P25.3) MUTATED                                  0     1
  DEL PEAK  3(2P25.3) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  3(2P25.3) MUTATED                           7
  DEL PEAK  3(2P25.3) WILD-TYPE                        94
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  3(2P25.3) MUTATED                                           1    16
  DEL PEAK  3(2P25.3) WILD-TYPE                                         8   350
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                                                              16
                                           clus
vv                                          DEL PEAK  3(2P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            94
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               350
[1] 5 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  20
  DEL PEAK  3(2P25.3) WILD-TYPE  14 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      0   20
  DEL PEAK  3(2P25.3) WILD-TYPE   14  347
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          20
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           347
[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    30  16
  DEL PEAK  4(2Q22.1) WILD-TYPE 427  53
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           46                           480 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           16                            53 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-5B-A90C TCGA-AJ-A23M TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3QS TCGA-AJ-A3TW 
       36.69         1.18        34.16         1.12        16.87        16.87 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0L9 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW 
       21.99        45.53       125.42        36.13         0.56        37.78 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A3G1 TCGA-B5-A0JN TCGA-B5-A1MS 
       11.08         4.77        30.12        20.52        80.38       102.31 
TCGA-B5-A1MY TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 
       11.87        29.65        34.13        15.45         6.81        10.16 
TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-D1-A16I TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
        4.80        67.20        11.51         2.07         4.27         4.11 
TCGA-DI-A1NO TCGA-EO-A1Y7 TCGA-EO-A2CH TCGA-EY-A1GC TCGA-EY-A1GR TCGA-EY-A1GW 
        9.37        49.15        19.40         4.54        17.62        11.08 
TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A4KR TCGA-FI-A3PV 
       10.19        20.05        29.10        13.84        11.38        41.06 
TCGA-H5-A2HR TCGA-KP-A3VZ TCGA-PG-A5BC TCGA-PG-A915 
        1.74        23.74        23.24         7.00 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 
        7.92        11.44        36.33         9.60         8.02        91.04 
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-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN 
       14.43        10.26         0.39        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
       34.36         0.76        18.90         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        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        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        46.78        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        21.90        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-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-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82         0.20         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47         0.39        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       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        27.29        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-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      191.84        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-A3FH TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        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        22.06        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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
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-A160 TCGA-D1-A161 TCGA-D1-A163 
       30.08        29.88         1.91         3.68        29.33        32.58 
TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 TCGA-D1-A16B TCGA-D1-A16D 
        0.66        15.72        36.10        37.32        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       36.79        27.42        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 
       18.02        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
        8.48        44.88         0.26        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       12.39        31.10       110.10        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        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        51.42        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW 
       17.19        27.16        17.88        26.96        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        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-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-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 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         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-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 
       29.23        45.01         7.76        14.04         2.43        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
        9.47        26.10        18.21        15.45        23.97        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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       16.870                        23.885 
[1] "0.6 - 125.4 (16.9)" "0.1 - 191.8 (23.9)"
[1] "hr=" "4.1"
D55V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                        17
  DEL PEAK  4(2Q22.1) WILD-TYPE                                     378
                               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                                  27
  DEL PEAK  4(2Q22.1) WILD-TYPE                                85
D55V3, multiclass
                                         clus
vv                                        DEL PEAK  4(2Q22.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          17
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                27
                                         clus
vv                                        DEL PEAK  4(2Q22.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           378
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     4  42
  DEL PEAK  4(2Q22.1) WILD-TYPE 137 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      4   42
  DEL PEAK  4(2Q22.1) WILD-TYPE  137  345
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            4                           137
  YES                          42                           345
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED    24   2   5   7
  DEL PEAK  4(2Q22.1) WILD-TYPE 339  21  12  28
D55V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                          24                           339
  R1                           2                            21
  R2                           5                            12
  RX                           7                            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  4(2Q22.1) MUTATED                                  0     1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  4(2Q22.1) MUTATED                          16
  DEL PEAK  4(2Q22.1) WILD-TYPE                        85
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  4(2Q22.1) MUTATED                                           1    26
  DEL PEAK  4(2Q22.1) WILD-TYPE                                         8   340
D55V6, multiclass
                                           clus
vv                                          DEL PEAK  4(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              26
                                           clus
vv                                          DEL PEAK  4(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               340
[1] 5 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  34
  DEL PEAK  4(2Q22.1) WILD-TYPE  13 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1   34
  DEL PEAK  4(2Q22.1) WILD-TYPE   13  333
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           333
[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    39  12
  DEL PEAK  5(2Q37.3) WILD-TYPE 418  57
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           51                           475 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           12                            57 
$`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        34.16         0.76        18.90 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW 
       22.26        17.06        20.81        21.21        16.87        16.87 
TCGA-AP-A05A TCGA-AP-A0LI TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A1CF TCGA-AX-A2H4 
       63.91        97.71        21.90         0.56        76.83        30.12 
TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-B5-A0KB TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-BG-A0M8 
       43.82        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 
       49.15        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-KP-A3VZ 
       15.81        11.08        29.10        14.70        41.06        23.74 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       23.97         7.00         4.44 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        60.53        46.55 
TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       38.37        28.27        20.81        23.21        68.65        19.96 
TCGA-A5-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-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-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        1.12         1.68         1.64        14.66        22.49        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        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-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        46.78        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        36.13        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-A1CI 
       13.55        15.25        20.28        12.43        20.05        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-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 
       64.93         0.23         0.20         0.56         0.20         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        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        20.02        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-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-A16I TCGA-D1-A16J 
       37.32        36.36        37.51        36.79        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       36.62        24.30        35.38        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE 
       14.53        24.89         6.21        14.99        53.88        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-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        17.92        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         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-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
       25.02        29.23        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        13.28         9.47        26.10        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       12.92        23.64        14.83        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       102.31                        191.84 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                        22.26                         23.34 
[1] "0.6 - 102.3 (22.3)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.1"
D56V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  5(2Q37.3) MUTATED                                        26
  DEL PEAK  5(2Q37.3) WILD-TYPE                                     369
                               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                                  24
  DEL PEAK  5(2Q37.3) WILD-TYPE                                88
D56V3, multiclass
                                         clus
vv                                        DEL PEAK  5(2Q37.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          26
  MIXED SEROUS AND ENDOMETRIOID                                     2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                24
                                         clus
vv                                        DEL PEAK  5(2Q37.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           369
  MIXED SEROUS AND ENDOMETRIOID                                      19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  88
[1] 3 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  43
  DEL PEAK  5(2Q37.3) WILD-TYPE 132 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      9   43
  DEL PEAK  5(2Q37.3) WILD-TYPE  132  344
     clus
vv    DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  NO                            9                           132
  YES                          43                           344
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.3) MUTATED    32   2   3   8
  DEL PEAK  5(2Q37.3) WILD-TYPE 331  21  14  27
D56V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  R0                          32                           331
  R1                           2                            21
  R2                           3                            14
  RX                           8                            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  5(2Q37.3) MUTATED                                  0     0
  DEL PEAK  5(2Q37.3) WILD-TYPE                                4    20
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  5(2Q37.3) MUTATED                          14
  DEL PEAK  5(2Q37.3) WILD-TYPE                        87
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  5(2Q37.3) MUTATED                                           2    32
  DEL PEAK  5(2Q37.3) WILD-TYPE                                         7   334
D56V6, multiclass
                                           clus
vv                                          DEL PEAK  5(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          14
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              32
                                           clus
vv                                          DEL PEAK  5(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                20
  BLACK OR AFRICAN AMERICAN                                            87
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  WHITE                                                               334
[1] 5 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  41
  DEL PEAK  5(2Q37.3) WILD-TYPE  13 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      1   41
  DEL PEAK  5(2Q37.3) WILD-TYPE   13  326
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           326
[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    64  12
  DEL PEAK  6(3P14.2) WILD-TYPE 393  57
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           76                           450 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                           12                            57 
$`DEL PEAK  6(3P14.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 
       41.06        36.69        37.02        11.44        36.33        46.32 
TCGA-AJ-A23M TCGA-AJ-A2QN TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3TW 
        1.18         2.40         1.12         1.64        21.21        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ 
       20.78        21.99        57.80       125.42        97.71        46.78 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1CF TCGA-AX-A1CP 
       21.90         0.56        53.92        37.78        76.83        36.39 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       11.08         4.77        71.24        61.18        19.36         1.38 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A1N2 
        0.39        80.38        27.29         4.11        75.72        12.79 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A4ZD 
       22.06        12.56        15.45         6.81        10.16        16.64 
TCGA-BS-A0TI TCGA-D1-A0ZZ TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NW TCGA-D1-A1O0 
       61.87        22.55        31.07        18.67         0.72         2.07 
TCGA-D1-A2G7 TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-EO-A1Y5 
       44.88        16.93        35.38        31.10        48.36        10.92 
TCGA-EO-A1Y7 TCGA-EO-A2CH TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP 
       49.15        19.40        16.34        23.90        19.27        18.84 
TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       17.62        15.81        29.10        27.35        13.84        11.38 
TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-JU-AAVI 
       14.70        39.95         9.07        28.93        25.02         7.76 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A915 TCGA-SL-A6J9 
       26.10        18.21         7.00         0.07 

$`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 
       10.29       106.88       149.56        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ 
      112.54       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        14.43        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       34.36        34.16         0.76        18.90         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        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       22.32        12.82         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        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91        48.79       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-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        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-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-A1CI 
       13.55        15.25        20.28        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2HA 
       54.12        67.50        25.12        30.12        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        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-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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-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         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-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-A3DA 
        1.05         3.95         3.52        41.42         8.48         0.26 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        24.30         9.37        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       23.38        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       35.15        17.19        27.16        17.88        26.96        22.26 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
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-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW 
        6.90        17.88        15.09        16.11        12.43        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A547 TCGA-EY-A548 
       22.82        20.05        45.76        31.04        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        16.96         5.88        40.01        41.06        39.88 
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-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KJ-A3U4 
       29.23        41.06        45.01         1.74        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 
       23.74        13.28         9.47        23.24        15.45        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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83         4.44        14.07        18.28         0.23 

  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                         0.07                          0.13 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE 
                        20.09                         23.72 
[1] "0.1 - 125.4 (20.1)" "0.1 - 191.8 (23.7)"
[1] "hr=" "1.4"
D57V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  6(3P14.2) MUTATED                                        27
  DEL PEAK  6(3P14.2) WILD-TYPE                                     368
                               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                                  44
  DEL PEAK  6(3P14.2) WILD-TYPE                                68
D57V3, multiclass
                                         clus
vv                                        DEL PEAK  6(3P14.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          27
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                44
                                         clus
vv                                        DEL PEAK  6(3P14.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           368
  MIXED SEROUS AND ENDOMETRIOID                                      15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V4, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED    16  61
  DEL PEAK  6(3P14.2) WILD-TYPE 125 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED     16   61
  DEL PEAK  6(3P14.2) WILD-TYPE  125  326
     clus
vv    DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  NO                           16                           125
  YES                          61                           326
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P14.2) MUTATED    55   3   4   5
  DEL PEAK  6(3P14.2) WILD-TYPE 308  20  13  30
D57V5, multiclass
    clus
vv   DEL PEAK  6(3P14.2) MUTATED DEL PEAK  6(3P14.2) WILD-TYPE
  R0                          55                           308
  R1                           3                            20
  R2                           4                            13
  RX                           5                            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
  DEL PEAK  6(3P14.2) MUTATED                                  0     1
  DEL PEAK  6(3P14.2) WILD-TYPE                                4    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  6(3P14.2) MUTATED                          25
  DEL PEAK  6(3P14.2) WILD-TYPE                        76
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  6(3P14.2) MUTATED                                           0    47
  DEL PEAK  6(3P14.2) WILD-TYPE                                         9   319
D57V6, multiclass
                                           clus
vv                                          DEL PEAK  6(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           0
  WHITE                                                              47
                                           clus
vv                                          DEL PEAK  6(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            76
  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"
D57V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P14.2) MUTATED     0  58
  DEL PEAK  6(3P14.2) WILD-TYPE  14 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P14.2) MUTATED      0   58
  DEL PEAK  6(3P14.2) WILD-TYPE   14  309
                        clus
vv                       DEL PEAK  6(3P14.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          58
                        clus
vv                       DEL PEAK  6(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           309
[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   5
  DEL PEAK  7(3Q13.31) WILD-TYPE 420  64
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            42                            484 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                             5                             64 
$`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 
       16.87        45.53       125.42        31.73        46.78        36.13 
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         0.30 
TCGA-AX-A3G7 TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11F TCGA-B5-A11W TCGA-B5-A5OD 
        0.30        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 TCGA-KP-A3VZ TCGA-QS-A8F1 
       18.84        29.10        39.95         1.74        23.74         4.44 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
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-A2K4 TCGA-A5-A2K5 
        7.92         9.60         8.02        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        14.43        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       19.79        29.39         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         1.68         1.64        14.66        22.49 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV 
       10.19        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD 
       36.89        23.87        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-A0LL 
      110.37         3.39        63.16        36.36        97.71        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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       16.24        21.90        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-A1CC TCGA-AX-A1CE 
       19.20        16.96        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-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       11.08         4.77        30.12        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
       43.82         0.20         1.38         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        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        27.29        17.88        13.74        17.10        11.01 
TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11G TCGA-B5-A11H TCGA-B5-A11I TCGA-B5-A11J 
        4.11         8.71       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-A11Y TCGA-B5-A11Z TCGA-B5-A121 
       27.35        16.73        19.56        18.41        17.36        16.57 
TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX 
      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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       62.14        33.11        14.27        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       22.06        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        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98        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-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-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-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        0.72        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-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
       39.29        36.62        24.30        35.38         9.37        12.39 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10       110.10        23.38        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        19.40        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        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-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 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       13.84        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         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-FI-A3PX TCGA-JU-AAVI 
       28.96        25.02        29.23        41.06        45.01         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 
       14.04         2.43        13.28         9.47        26.10        18.21 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       23.24        15.45        23.97        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                          0.30                           0.07 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        185.79                         191.84 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                         21.39                          23.36 
[1] "0.3 - 185.8 (21.4)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.1"
D58V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  7(3Q13.31) MUTATED                                        17
  DEL PEAK  7(3Q13.31) WILD-TYPE                                     378
                                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                                  22
  DEL PEAK  7(3Q13.31) WILD-TYPE                                90
D58V3, multiclass
                                         clus
vv                                        DEL PEAK  7(3Q13.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           17
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 22
                                         clus
vv                                        DEL PEAK  7(3Q13.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            378
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     8  34
  DEL PEAK  7(3Q13.31) WILD-TYPE 133 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      8   34
  DEL PEAK  7(3Q13.31) WILD-TYPE  133  353
     clus
vv    DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  NO                             8                            133
  YES                           34                            353
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  7(3Q13.31) MUTATED    28   1   0   3
  DEL PEAK  7(3Q13.31) WILD-TYPE 335  22  17  32
D58V5, multiclass
    clus
vv   DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  R0                           28                            335
  R1                            1                             22
  R2                            0                             17
  RX                            3                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q13.31) MUTATED                                  0     1
  DEL PEAK  7(3Q13.31) WILD-TYPE                                4    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK  7(3Q13.31) MUTATED                          10
  DEL PEAK  7(3Q13.31) WILD-TYPE                        91
                                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      28
  DEL PEAK  7(3Q13.31) WILD-TYPE   338
D58V6, multiclass
                                           clus
vv                                          DEL PEAK  7(3Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               28
                                           clus
vv                                          DEL PEAK  7(3Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                338
[1] 5 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  26
  DEL PEAK  7(3Q13.31) WILD-TYPE  13 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      1   26
  DEL PEAK  7(3Q13.31) WILD-TYPE   13  341
                        clus
vv                       DEL PEAK  7(3Q13.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK  7(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            341
[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    69  19
  DEL PEAK  8(4P16.3) WILD-TYPE 388  50
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           88                           438 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           19                            50 
$`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        34.16         1.64        21.21 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H 
       10.19        16.87        16.87         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        21.90         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         0.30        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         3.95        14.73        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QT TCGA-EO-A1Y7 
        0.72        18.25        16.93        35.38        12.39        49.15 
TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR 
       27.16        22.26        16.34        19.27        18.84        17.62 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR 
       10.19        14.40        20.05        45.76        27.35        11.38 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.07        28.93        25.02        29.23        41.06        45.01 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
        7.76        14.04        23.74        13.28         9.47        26.10 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 
       23.24        23.97         7.00         4.44 

$`DEL PEAK  8(4P16.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        65.75        60.53        46.55        38.37        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-A1OH 
       29.06        42.35        15.95         7.92        11.44        36.33 
TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M 
        9.60         8.02        46.32         5.33         5.16         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       14.43        10.26        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76        18.90         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        17.06        20.81        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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-A0L8 
        8.22        63.91        23.87        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-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        46.78        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        36.13        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-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-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        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13        64.93         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.56        43.82         0.20         1.38         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        80.38        56.91 
TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JY TCGA-B5-A0JZ 
       46.75        43.13        48.76        40.67        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        27.29        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        11.01         4.11         8.71       185.79       113.36 
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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        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-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-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         6.21        10.22        10.16        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-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-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-A15W TCGA-D1-A15X TCGA-D1-A15Z TCGA-D1-A160 TCGA-D1-A161 
       21.99        30.08        29.88         1.91         3.68        29.33 
TCGA-D1-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX 
       36.62        24.30         9.37        31.10       110.10        23.38 
TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ 
       48.36        17.06         2.37         6.67        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 
       34.39        26.43        35.15        17.19        17.88        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
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-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       13.97         6.90        17.88        15.09        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       15.81        11.08         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 
       22.82        31.04        29.10        13.84        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3W4 TCGA-PG-A6IB 
       59.01        28.96         1.74         2.43        18.21        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       20.005                        23.885 
[1] "0.2 - 149.6 (20.0)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.3"
D59V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                        29
  DEL PEAK  8(4P16.3) WILD-TYPE                                     366
                               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                                  55
  DEL PEAK  8(4P16.3) WILD-TYPE                                57
D59V3, multiclass
                                         clus
vv                                        DEL PEAK  8(4P16.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          29
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                55
                                         clus
vv                                        DEL PEAK  8(4P16.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           366
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    20  69
  DEL PEAK  8(4P16.3) WILD-TYPE 121 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     20   69
  DEL PEAK  8(4P16.3) WILD-TYPE  121  318
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  NO                           20                           121
  YES                          69                           318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4P16.3) MUTATED    63   4   4   5
  DEL PEAK  8(4P16.3) WILD-TYPE 300  19  13  30
D59V5, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  R0                          63                           300
  R1                           4                            19
  R2                           4                            13
  RX                           5                            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
  DEL PEAK  8(4P16.3) MUTATED                                  1     1
  DEL PEAK  8(4P16.3) WILD-TYPE                                3    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  8(4P16.3) MUTATED                          16
  DEL PEAK  8(4P16.3) WILD-TYPE                        85
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  8(4P16.3) MUTATED                                           3    61
  DEL PEAK  8(4P16.3) WILD-TYPE                                         6   305
D59V6, multiclass
                                           clus
vv                                          DEL PEAK  8(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              61
                                           clus
vv                                          DEL PEAK  8(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  WHITE                                                               305
[1] 5 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  67
  DEL PEAK  8(4P16.3) WILD-TYPE  11 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      3   67
  DEL PEAK  8(4P16.3) WILD-TYPE   11  300
                        clus
vv                       DEL PEAK  8(4P16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK  8(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           300
[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    71  21
  DEL PEAK  9(4P15.2) WILD-TYPE 386  48
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           92                           434 
  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                           21                            48 
$`DEL PEAK  9(4P15.2) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A2K2 
       36.69       149.56        60.53        36.82        19.96        91.04 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3EJ 
       28.64         7.33        14.96         0.39        34.16         1.64 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05D 
       21.21        10.19        16.87        16.87         5.95        57.80 
TCGA-AP-A05H TCGA-AP-A0LF TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B 
       45.53         3.39        33.40        21.90         0.56        53.92 
TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 
       37.78        20.28        12.43        76.83        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G3 
       30.12        19.36         2.96         0.23        20.52         1.38 
TCGA-B5-A0JX TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A3S1 
       44.71        17.85        75.72        36.82        11.87        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC 
       34.13        34.95        36.49        12.56         6.81        10.22 
TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A169 
       24.13        61.87        67.20        49.55        39.48        37.32 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NW TCGA-D1-A3JP TCGA-DI-A1NN 
       18.67         3.95        14.73         0.72        16.93        35.38 
TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KU 
       12.39       110.10        49.15        34.39        27.16        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A212 
       16.34         4.54        19.27        18.84        17.62        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       14.40        20.05        45.76        27.35        13.84        11.38 
TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ 
        9.07        25.02        41.06         7.76        14.04        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
       13.28         9.47        26.10        18.21        23.24        23.97 
TCGA-PG-A915 TCGA-QS-A8F1 
        7.00         4.44 

$`DEL PEAK  9(4P15.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-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-AJ-A23M TCGA-AJ-A23N 
        8.02        46.32         5.33         5.16         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26        19.79        29.39         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76        18.90         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       17.06        20.81        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       15.95        14.76        22.32        12.82        20.78         2.70 
TCGA-AJ-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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       63.91        36.89        23.87        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-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        46.78        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        36.13        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-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE 
       13.28        19.20        16.96        13.55        15.25        20.05 
TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 
       72.56        54.12        67.50        25.12        36.39        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       40.80        61.18        81.37        34.32        46.49        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW 
       17.75        30.74        31.13        64.93         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       43.82         0.20         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        80.38        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        27.29        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-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-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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        14.27        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        22.06        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-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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 
       20.12        11.31        35.90        34.98         6.21        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-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-A1NU TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41        13.22        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-A2KV 
        8.48        44.88         0.26         4.27         4.11        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
        9.37        31.10        23.38        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        27.32        16.04         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        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        19.40        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        26.96        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-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-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 
       18.87        22.82        31.04        29.10        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       19.89        14.70        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       39.88        39.95         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       59.01        28.93        28.96        29.23        45.01         1.74 
TCGA-KJ-A3U4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
        2.43        15.45        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE 
                         0.23                          0.07 
  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 
                       20.005                        23.885 
[1] "0.2 - 149.6 (20.0)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.4"
D60V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK  9(4P15.2) MUTATED                                        31
  DEL PEAK  9(4P15.2) WILD-TYPE                                     364
                               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                                  57
  DEL PEAK  9(4P15.2) WILD-TYPE                                55
D60V3, multiclass
                                         clus
vv                                        DEL PEAK  9(4P15.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          31
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                57
                                         clus
vv                                        DEL PEAK  9(4P15.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           364
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED    18  75
  DEL PEAK  9(4P15.2) WILD-TYPE 123 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED     18   75
  DEL PEAK  9(4P15.2) WILD-TYPE  123  312
     clus
vv    DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  NO                           18                           123
  YES                          75                           312
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P15.2) MUTATED    60   4   5   7
  DEL PEAK  9(4P15.2) WILD-TYPE 303  19  12  28
D60V5, multiclass
    clus
vv   DEL PEAK  9(4P15.2) MUTATED DEL PEAK  9(4P15.2) WILD-TYPE
  R0                          60                           303
  R1                           4                            19
  R2                           5                            12
  RX                           7                            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  9(4P15.2) MUTATED                                  1     1
  DEL PEAK  9(4P15.2) WILD-TYPE                                3    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK  9(4P15.2) MUTATED                          21
  DEL PEAK  9(4P15.2) WILD-TYPE                        80
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK  9(4P15.2) MUTATED                                           2    60
  DEL PEAK  9(4P15.2) WILD-TYPE                                         7   306
D60V6, multiclass
                                           clus
vv                                          DEL PEAK  9(4P15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              60
                                           clus
vv                                          DEL PEAK  9(4P15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  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"
D60V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P15.2) MUTATED     4  67
  DEL PEAK  9(4P15.2) WILD-TYPE  10 300
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P15.2) MUTATED      4   67
  DEL PEAK  9(4P15.2) WILD-TYPE   10  300
                        clus
vv                       DEL PEAK  9(4P15.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          67
                        clus
vv                       DEL PEAK  9(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           300
[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    79  22
  DEL PEAK 10(4Q22.1) WILD-TYPE 378  47
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          101                           425 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           22                            47 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       36.69       149.56        65.75        60.53        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       11.44        36.33        91.04        28.64         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH 
       14.43        29.39        34.16         1.64        21.21        10.19 
TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF 
       21.99        57.80        45.53        48.79       125.42         3.39 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
       97.71        33.40        37.78        13.55        20.28        12.43 
TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF 
       76.83        11.08         4.77        30.12        61.18        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        2.96        64.93         0.23        20.52         1.38         0.30 
TCGA-AX-A3G7 TCGA-B5-A0JN TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MU 
        0.30        80.38        75.72        36.82       102.31        50.89 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M8 
       11.87        12.79        33.11        29.65        34.13        36.49 
TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 
       12.56         6.81        10.22        24.13        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         3.95        14.73        13.22 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
        4.27         4.11        16.93        35.38         9.37       110.10 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GC TCGA-EY-A1GM 
       51.42        27.16        26.96        22.26         4.54         6.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A214 
       19.27        18.84        17.62        15.09        10.19        14.40 
TCGA-EY-A2OO TCGA-EY-A3QX TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A2EY 
       45.76        13.84         5.88        41.06         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       25.02        41.06         7.76         2.43        23.74        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        12.92         7.00 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16        14.96        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       34.36         1.12         0.76        18.90         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        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J 
        5.95        23.31        86.07         8.22        63.91        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG 
       23.87        12.20        20.91       117.99       110.37        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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX 
       30.90        10.42        27.85        16.24        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        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-A1C9 TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       16.96        15.25        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12        36.39        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FT 
       46.49        26.33        17.75        30.74        31.13         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56        43.82         0.20         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        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        27.29        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-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-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       191.84        14.40        14.70        11.70        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        14.27        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-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        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-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-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         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-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-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-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
       10.65         0.69         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-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-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        0.26        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30        12.39        31.10        23.38        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        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
       16.80        10.92        49.15        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX 
       26.43        35.15        17.19        17.88        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        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        11.08         6.48        19.33 
TCGA-EY-A210 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ 
       12.59        18.87        22.82        20.05        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       27.35        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96        40.01        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PX 
        8.98        96.69        59.01        28.96        29.23        45.01 
TCGA-H5-A2HR TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 
        1.74        14.04         9.47        15.45        23.97        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        21.21                         23.47 
[1] "0.2 - 149.6 (21.2)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2"  
D61V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                        30
  DEL PEAK 10(4Q22.1) WILD-TYPE                                     365
                               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                                  66
  DEL PEAK 10(4Q22.1) WILD-TYPE                                46
D61V3, multiclass
                                         clus
vv                                        DEL PEAK 10(4Q22.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          30
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                66
                                         clus
vv                                        DEL PEAK 10(4Q22.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           365
  MIXED SEROUS AND ENDOMETRIOID                                      15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V4, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    21  81
  DEL PEAK 10(4Q22.1) WILD-TYPE 120 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     21   81
  DEL PEAK 10(4Q22.1) WILD-TYPE  120  306
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                           21                           120
  YES                          81                           306
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED    63   6   7   7
  DEL PEAK 10(4Q22.1) WILD-TYPE 300  17  10  28
D61V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                          63                           300
  R1                           6                            17
  R2                           7                            10
  RX                           7                            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 10(4Q22.1) MUTATED                                  0     3
  DEL PEAK 10(4Q22.1) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 10(4Q22.1) MUTATED                          26
  DEL PEAK 10(4Q22.1) WILD-TYPE                        75
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 10(4Q22.1) MUTATED                                           3    65
  DEL PEAK 10(4Q22.1) WILD-TYPE                                         6   301
D61V6, multiclass
                                           clus
vv                                          DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              65
                                           clus
vv                                          DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  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"
D61V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     3  70
  DEL PEAK 10(4Q22.1) WILD-TYPE  11 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      3   70
  DEL PEAK 10(4Q22.1) WILD-TYPE   11  297
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          70
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           297
[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   101  25
  DEL PEAK 11(4Q34.3) WILD-TYPE 356  44
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                          126                           400 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                           25                            44 
$`DEL PEAK 11(4Q34.3) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       36.69       149.56        65.75        60.53        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       11.44        36.33        91.04        28.64         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH 
       14.43        29.39        34.16         1.64        20.81        10.19 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05D TCGA-AP-A05H 
       16.87        16.87        20.78        21.99        57.80        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A1DQ 
       48.79       125.42         3.39        97.71        33.40        46.78 
TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC 
       36.13         0.56        37.78        13.55        20.28        12.43 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2IO 
       11.08         4.77        30.12        61.18        19.36        64.93 
TCGA-AX-A3FS TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN 
        0.23        20.52         1.38         0.30         0.39        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-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE 
       11.87        12.79        33.11        29.65        34.13        34.95 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A222 TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L 
       36.49        12.56         9.57         6.81        10.22        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       16.64         4.80        61.87        67.20        49.55        22.55 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 
       39.48        37.32        31.07        18.67         3.95        14.73 
TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A3DG 
       28.08        13.22         0.72        16.87         2.07         4.27 
TCGA-D1-A3DH TCGA-DI-A0WH TCGA-DI-A1NN TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A22R 
        4.11        16.31        35.38       110.10        48.36        61.74 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       51.42        19.40        34.39        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS 
       16.34         6.90        19.27        18.84        17.62        15.09 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       10.19        14.40        45.76        29.10        27.35        13.84 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV 
       14.70         5.88         9.07        28.93        25.02        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W3 
       45.01         1.74         7.76         2.43        23.74        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       18.21        23.24        23.97        12.92         7.00         4.44 

$`DEL PEAK 11(4Q34.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        5.16        14.96        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK 
       34.36         1.12         0.76        18.90         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        17.06        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-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-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
        8.22        63.91        36.89        23.87        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-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-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 
       21.90        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-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       16.96        15.25        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-A2HA 
       67.50        25.12        36.39        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 
       31.13         0.20         0.56        43.82         0.20         0.26 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        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        27.29        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-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-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
       16.57       191.84        14.40        14.70        11.70        15.29 
TCGA-B5-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
      116.25        96.30        78.81        62.14        14.27        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 
       22.06        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-A2AD 
       14.01        15.45        15.45        14.27         1.81        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-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-A1NX TCGA-D1-A1NZ 
       24.30         2.33        22.92         1.41        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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
       44.88         0.26        16.93        89.33        10.92        27.16 
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        27.32        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22S 
        7.36        16.80        10.92        49.15        37.71        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV 
       66.90        46.26        57.60        51.52        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.19        17.88        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU 
       23.90        22.78        13.97        17.88        16.11        12.43 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       15.81        11.08         6.48        19.33        12.59        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       22.82        20.05        31.04        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       19.89        16.96        40.01        41.06        39.88        39.95 
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-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A916 
       29.23        14.04        13.28         9.47        15.45        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE 
                       20.795                        23.670 
[1] "0.2 - 149.6 (20.8)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2"  
D62V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 11(4Q34.3) MUTATED                                        43
  DEL PEAK 11(4Q34.3) WILD-TYPE                                     352
                               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                                  76
  DEL PEAK 11(4Q34.3) WILD-TYPE                                36
D62V3, multiclass
                                         clus
vv                                        DEL PEAK 11(4Q34.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          43
  MIXED SEROUS AND ENDOMETRIOID                                     8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                76
                                         clus
vv                                        DEL PEAK 11(4Q34.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           352
  MIXED SEROUS AND ENDOMETRIOID                                      13
  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"
D62V4, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q34.3) MUTATED    27 100
  DEL PEAK 11(4Q34.3) WILD-TYPE 114 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q34.3) MUTATED     27  100
  DEL PEAK 11(4Q34.3) WILD-TYPE  114  287
     clus
vv    DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE
  NO                           27                           114
  YES                         100                           287
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q34.3) MUTATED    81   6   8   7
  DEL PEAK 11(4Q34.3) WILD-TYPE 282  17   9  28
D62V5, multiclass
    clus
vv   DEL PEAK 11(4Q34.3) MUTATED DEL PEAK 11(4Q34.3) WILD-TYPE
  R0                          81                           282
  R1                           6                            17
  R2                           8                             9
  RX                           7                            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 11(4Q34.3) MUTATED                                  0     4
  DEL PEAK 11(4Q34.3) WILD-TYPE                                4    16
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 11(4Q34.3) MUTATED                          37
  DEL PEAK 11(4Q34.3) WILD-TYPE                        64
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 11(4Q34.3) MUTATED                                           3    75
  DEL PEAK 11(4Q34.3) WILD-TYPE                                         6   291
D62V6, multiclass
                                           clus
vv                                          DEL PEAK 11(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               4
  BLACK OR AFRICAN AMERICAN                                          37
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              75
                                           clus
vv                                          DEL PEAK 11(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                16
  BLACK OR AFRICAN AMERICAN                                            64
  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"
D62V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q34.3) MUTATED     3  88
  DEL PEAK 11(4Q34.3) WILD-TYPE  11 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q34.3) MUTATED      3   88
  DEL PEAK 11(4Q34.3) WILD-TYPE   11  279
                        clus
vv                       DEL PEAK 11(4Q34.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       DEL PEAK 11(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           279
[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    85  23
  DEL PEAK 12(5Q12.1) WILD-TYPE 372  46
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          108                           418 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           23                            46 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A0R7 
       41.06        36.69       149.56        65.75        19.96        17.59 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A2QK 
       11.44        36.33         7.33        14.96         1.18         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3NF 
       29.39        34.16         1.64        22.26        20.81        21.21 
TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       10.19        16.87        16.87        45.53        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B 
        3.39        97.71        33.40        21.90        36.13        53.92 
TCGA-AX-A0IW TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H4 
       37.78        13.55        20.28        76.83         4.77        30.12 
TCGA-AX-A2HF TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 
       19.36        43.82         0.20        20.52         0.30         0.26 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A11I TCGA-B5-A1MU TCGA-B5-A1N2 
        0.39        80.38        17.85        75.72        50.89        12.79 
TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 
       33.11        29.65        34.13        34.95        22.06        36.49 
TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       12.56         6.81        10.22        10.16        24.13        16.64 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A15V TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S 
       67.20        49.55        39.48        11.51        31.07        18.67 
TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-DI-A1NO 
       14.73        13.22        18.25         2.07        16.93         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       31.10       110.10        48.36        27.32        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       37.71        51.42        34.39        27.16        26.96        22.26 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A212 
       23.90        19.27        18.84        17.62        11.08        10.19 
TCGA-EY-A214 TCGA-EY-A3QX TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY 
       14.40        13.84        17.92        39.95        96.69        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       25.02        41.06        45.01        14.04         2.43        23.74 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
        9.47        26.10        23.24        12.92         7.00         4.44 

$`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 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
      112.54       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        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36         1.12         0.76        18.90         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       14.66        22.49        17.06        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.35        15.95        14.76        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        63.91        57.80        36.89        23.87 
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-A1DO TCGA-AP-A1DP TCGA-AP-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        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-A1C7 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        16.96        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-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.23         0.20         0.56         1.38         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       18.35        14.47        56.91        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        27.29        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-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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       14.27        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-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-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98         6.21        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-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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       27.42        29.92        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV 
        8.48        44.88         0.26         4.27         4.11        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       35.38        12.39        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.04         7.36        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.52        19.40        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.19        17.88        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GS 
       23.34        22.78        13.97         6.90        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-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        11.38        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR 
        8.98        59.01         9.07        28.96        29.23         1.74 
TCGA-JU-AAVI TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 
        7.76        13.28        18.21        15.45        23.97        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       149.56                        191.84 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       21.980                        23.555 
[1] "0.2 - 149.6 (22.0)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2"  
D63V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                        35
  DEL PEAK 12(5Q12.1) WILD-TYPE                                     360
                               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                                  70
  DEL PEAK 12(5Q12.1) WILD-TYPE                                42
D63V3, multiclass
                                         clus
vv                                        DEL PEAK 12(5Q12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          35
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                70
                                         clus
vv                                        DEL PEAK 12(5Q12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           360
  MIXED SEROUS AND ENDOMETRIOID                                      17
  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"
D63V4, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    24  85
  DEL PEAK 12(5Q12.1) WILD-TYPE 117 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     24   85
  DEL PEAK 12(5Q12.1) WILD-TYPE  117  302
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                           24                           117
  YES                          85                           302
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED    69   4   4   9
  DEL PEAK 12(5Q12.1) WILD-TYPE 294  19  13  26
D63V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                          69                           294
  R1                           4                            19
  R2                           4                            13
  RX                           9                            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 12(5Q12.1) MUTATED                                  0     3
  DEL PEAK 12(5Q12.1) WILD-TYPE                                4    17
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 12(5Q12.1) MUTATED                          29
  DEL PEAK 12(5Q12.1) WILD-TYPE                        72
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 12(5Q12.1) MUTATED                                           3    64
  DEL PEAK 12(5Q12.1) WILD-TYPE                                         6   302
D63V6, multiclass
                                           clus
vv                                          DEL PEAK 12(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               3
  BLACK OR AFRICAN AMERICAN                                          29
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              64
                                           clus
vv                                          DEL PEAK 12(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                17
  BLACK OR AFRICAN AMERICAN                                            72
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  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"
D63V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     5  77
  DEL PEAK 12(5Q12.1) WILD-TYPE   9 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      5   77
  DEL PEAK 12(5Q12.1) WILD-TYPE    9  290
                        clus
vv                       DEL PEAK 12(5Q12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       DEL PEAK 12(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           290
[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    34  10
  DEL PEAK 13(6Q26) WILD-TYPE 423  59
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         44                         482 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         10                          59 
$`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        14.43        29.39 
TCGA-AJ-A3BF TCGA-AJ-A3EJ TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AP-A05J TCGA-AP-A0L9 
        1.12         1.64        10.19        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 
       64.93         1.38        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 
      110.10        48.36        27.32        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        11.38        39.95        41.06         1.74 
TCGA-KP-A3W0 TCGA-PG-A7D5 
       13.28        23.97 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        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-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96         1.18        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI 
       19.79         2.40        34.36        34.16         0.76        18.90 
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        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       14.76        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-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        63.91        57.80        45.53        23.87        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        46.78 
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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W 
       21.90        36.13        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-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-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A1CR 
       76.83        72.56        54.12        67.50        36.39        11.08 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        40.80        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 
       25.91        27.29        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-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-A1MV TCGA-B5-A1MW 
       17.36        16.57       191.84       102.31        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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       62.14        33.11        14.27        29.65        41.06        34.13 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        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        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B 
       35.90        34.98         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-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-A0V7 TCGA-BS-A0V8 TCGA-BS-A0VI TCGA-BS-A0WQ TCGA-D1-A0ZN 
       59.51        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-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-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S 
       27.42        31.07        33.63        10.65         0.69        18.67 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 
       13.22         0.72        18.25        16.87        18.02         2.07 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A1NO TCGA-DI-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-A1Y7 
        6.67        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CG 
       61.74        61.55        66.90        46.26        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       19.40        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       22.26        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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 
       11.08         6.48        19.33        12.59        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 
       18.87        22.82        20.05        45.76        31.04        27.35 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        17.92        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         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-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       25.02        29.23        45.01         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       23.74         9.47        26.10        18.21        23.24        15.45 
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 TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.56                        0.07 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     149.56                      191.84 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     27.140                      23.225 
[1] "0.6 - 149.6 (27.1)" "0.1 - 191.8 (23.2)"
[1] "hr=" "1.6"
D64V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 13(6Q26) MUTATED                                        13
  DEL PEAK 13(6Q26) WILD-TYPE                                     382
                             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                                  29
  DEL PEAK 13(6Q26) WILD-TYPE                                83
D64V3, multiclass
                                         clus
vv                                        DEL PEAK 13(6Q26) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        13
  MIXED SEROUS AND ENDOMETRIOID                                   3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              29
                                         clus
vv                                        DEL PEAK 13(6Q26) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         382
  MIXED SEROUS AND ENDOMETRIOID                                    18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    10  35
  DEL PEAK 13(6Q26) WILD-TYPE 131 352
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     10   35
  DEL PEAK 13(6Q26) WILD-TYPE  131  352
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                         10                         131
  YES                        35                         352
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(6Q26) MUTATED    34   1   1   2
  DEL PEAK 13(6Q26) WILD-TYPE 329  22  16  33
D64V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  R0                        34                         329
  R1                         1                          22
  R2                         1                          16
  RX                         2                          33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q26) MUTATED                                  0     2
  DEL PEAK 13(6Q26) WILD-TYPE                                4    18
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 13(6Q26) MUTATED                           9
  DEL PEAK 13(6Q26) WILD-TYPE                        92
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 13(6Q26) MUTATED                                           0    28
  DEL PEAK 13(6Q26) WILD-TYPE                                         9   338
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                                                            28
                                           clus
vv                                          DEL PEAK 13(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    4
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                          92
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           9
  WHITE                                                             338
[1] 5 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  30
  DEL PEAK 13(6Q26) WILD-TYPE  14 337
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      0   30
  DEL PEAK 13(6Q26) WILD-TYPE   14  337
                        clus
vv                       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             0                          14
  NOT HISPANIC OR LATINO                        30                         337
[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    52  17
  DEL PEAK 14(7P22.3) WILD-TYPE 405  52
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           69                           457 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                           17                            52 
$`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        46.78        21.90         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        30.74 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        2.96        64.93        27.29        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 
        3.95         0.72        44.88        35.38         9.37       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       48.36        27.32        16.04        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ 
       34.39        22.26        10.19        14.40        45.76        29.10 
TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 
       41.06        59.01         9.07        28.93        25.02        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       41.06        45.01         1.74         2.43        23.74        13.28 
TCGA-PG-A5BC TCGA-PG-A915 TCGA-QS-A8F1 
       23.24         7.00         4.44 

$`DEL PEAK 14(7P22.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        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-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K3 
        7.92        11.44         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        14.43        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        1.12         0.76        18.90         1.68        14.66        22.49 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       22.26        17.06        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW 
       15.62        10.19        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05N 
       21.99        86.07         8.22        63.91        57.80        23.87 
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-A5FX TCGA-AX-A05S 
       30.90        10.42        27.85        16.24        36.13        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-A1CC 
       65.88        13.28        19.20        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-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       36.39        71.24        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        19.36        26.33        17.75        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.30         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW 
       14.27        29.65        41.06        34.13        34.95        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 
       20.19        19.33        20.94        35.21        34.98        22.06 
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-BK-A0C9 
        9.57        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       34.98         6.21        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-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-A169 
       29.33        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X 
       31.07        33.63        10.65         0.69        18.67         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NX 
       24.30         2.33        22.92         1.41        13.22        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
        3.52        41.42         8.48         0.26         4.27         4.11 
TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
       16.93        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 
       36.62        24.30        12.39        31.10        23.38        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        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-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-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
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        20.05 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       31.04        27.35        13.84        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
       19.89        14.70        16.96         5.88        40.01        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 
       39.95         7.99        13.84         8.98        96.69        28.96 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
        7.76        14.04         9.47        26.10        18.21        15.45 
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 TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       12.92        23.64        14.83        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                         0.56                          0.07 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                       110.10                        191.84 
  DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE 
                        23.24                         23.38 
[1] "0.6 - 110.1 (23.2)" "0.1 - 191.8 (23.4)"
[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                                     374
                               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                                  44
  DEL PEAK 14(7P22.3) WILD-TYPE                                68
D65V3, multiclass
                                         clus
vv                                        DEL PEAK 14(7P22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          21
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                44
                                         clus
vv                                        DEL PEAK 14(7P22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           374
  MIXED SEROUS AND ENDOMETRIOID                                      16
  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"
D65V4, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED    16  54
  DEL PEAK 14(7P22.3) WILD-TYPE 125 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED     16   54
  DEL PEAK 14(7P22.3) WILD-TYPE  125  333
     clus
vv    DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  NO                           16                           125
  YES                          54                           333
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(7P22.3) MUTATED    46   4   4   7
  DEL PEAK 14(7P22.3) WILD-TYPE 317  19  13  28
D65V5, multiclass
    clus
vv   DEL PEAK 14(7P22.3) MUTATED DEL PEAK 14(7P22.3) WILD-TYPE
  R0                          46                           317
  R1                           4                            19
  R2                           4                            13
  RX                           7                            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 14(7P22.3) MUTATED                                  0     2
  DEL PEAK 14(7P22.3) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 14(7P22.3) MUTATED                          21
  DEL PEAK 14(7P22.3) WILD-TYPE                        80
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 14(7P22.3) MUTATED                                           1    40
  DEL PEAK 14(7P22.3) WILD-TYPE                                         8   326
D65V6, multiclass
                                           clus
vv                                          DEL PEAK 14(7P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              40
                                           clus
vv                                          DEL PEAK 14(7P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            80
  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"
D65V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(7P22.3) MUTATED     2  46
  DEL PEAK 14(7P22.3) WILD-TYPE  12 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7P22.3) MUTATED      2   46
  DEL PEAK 14(7P22.3) WILD-TYPE   12  321
                        clus
vv                       DEL PEAK 14(7P22.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          46
                        clus
vv                       DEL PEAK 14(7P22.3) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           321
[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    34   5
  DEL PEAK 15(7Q11.22) WILD-TYPE 423  64
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                            39                            487 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                             5                             64 
$`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        34.16        10.19        16.87 
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        64.93 
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 
       10.19        45.76        29.10        17.92        96.69        59.01 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       29.23        41.06        45.01 

$`DEL PEAK 15(7Q11.22) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        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-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-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-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
        5.33         5.16         7.33        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         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        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        36.89        23.87        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        46.78        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        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        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-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       19.20        16.96        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-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
        4.77        30.12        71.24        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        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        27.29        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-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-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-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       41.06        34.13        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 
       20.94        35.21        34.98        22.06        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-A18C TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       15.45        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       27.42        11.51        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
        1.41        13.22         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27        16.93        89.33        10.92        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-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10       110.10        23.38        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       27.32        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       37.71        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        51.42        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        17.88        26.96        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        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        11.08         6.48        19.33        12.59        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        20.05        31.04        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       11.38        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         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-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        7.76        14.04         2.43        23.74        13.28         9.47 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        18.21        23.24        15.45        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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                          2.07                           0.07 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                         96.69                         191.84 
  DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE 
                         22.26                          23.34 
[1] "2.1 - 96.7 (22.3)"  "0.1 - 191.8 (23.3)"
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 15(7Q11.22) MUTATED                                        13
  DEL PEAK 15(7Q11.22) WILD-TYPE                                     382
                                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                                88
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                            382
  MIXED SEROUS AND ENDOMETRIOID                                       19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   88
[1] 3 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     9  30
  DEL PEAK 15(7Q11.22) WILD-TYPE 132 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(7Q11.22) MUTATED      9   30
  DEL PEAK 15(7Q11.22) WILD-TYPE  132  357
     clus
vv    DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE
  NO                             9                            132
  YES                           30                            357
[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 334  20  15  33
D66V5, multiclass
    clus
vv   DEL PEAK 15(7Q11.22) MUTATED DEL PEAK 15(7Q11.22) WILD-TYPE
  R0                           29                            334
  R1                            3                             20
  R2                            2                             15
  RX                            2                             33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(7Q11.22) MUTATED                                  0     0
  DEL PEAK 15(7Q11.22) WILD-TYPE                                4    20
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 15(7Q11.22) MUTATED                          10
  DEL PEAK 15(7Q11.22) WILD-TYPE                        91
                                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   342
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                                                                 20
  BLACK OR AFRICAN AMERICAN                                             91
  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"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(7Q11.22) MUTATED     1  27
  DEL PEAK 15(7Q11.22) WILD-TYPE  13 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(7Q11.22) MUTATED      1   27
  DEL PEAK 15(7Q11.22) WILD-TYPE   13  340
                        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                                 13
  NOT HISPANIC OR LATINO                            340
[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    41  12
  DEL PEAK 16(7Q31.1) WILD-TYPE 416  57
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           53                           473 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                           12                            57 
$`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        14.43        34.16 
TCGA-AJ-A3NH TCGA-AP-A05D TCGA-AP-A1DQ TCGA-AX-A0IW TCGA-AX-A1CA TCGA-AX-A1CR 
       10.19        57.80        46.78        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        22.06        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       110.10        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        10.19        20.05        45.76        11.38 
TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       14.70        96.69        59.01        29.23        41.06        45.01 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       23.24        23.97        12.92         7.00         0.07 

$`DEL PEAK 16(7Q31.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP 
       74.10        57.53        65.75        60.53        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-A0R7 TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ 
       17.59        19.59        24.62        29.06        42.35        15.95 
TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-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-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.33         5.16         7.33        14.96        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79        29.39         2.40        34.36         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         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 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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-A05H 
        5.95        23.31        86.07         8.22        63.91        45.53 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       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-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-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        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-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-A2H2 TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        0.23         0.20         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        1.38         0.30         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        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        27.29        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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       78.81        62.14        33.11        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       34.13        34.95        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-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-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        20.02        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       35.90        34.98         6.21        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-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-A169 TCGA-D1-A16B 
       32.58         0.66        15.72        36.10        37.32        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       37.51        36.79        27.42        11.51        29.92        31.07 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ 
        2.33        22.92         1.41         0.72        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 
       15.06         1.05         3.95         3.52        41.42         8.48 
TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27        16.93        89.33        10.92        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-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        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       51.42        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-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-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
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-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        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2EY 
       39.95         7.99        13.84         8.98         9.07        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 
       28.96        25.02         1.74         7.76        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       23.74        13.28         9.47        26.10        18.21        15.45 
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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.23 

  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                         0.07                          0.13 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                       110.10                        191.84 
  DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE 
                        22.06                         23.47 
[1] "0.1 - 110.1 (22.1)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2"  
D67V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 16(7Q31.1) MUTATED                                        10
  DEL PEAK 16(7Q31.1) WILD-TYPE                                     385
                               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                                72
D67V3, multiclass
                                         clus
vv                                        DEL PEAK 16(7Q31.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          10
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                40
                                         clus
vv                                        DEL PEAK 16(7Q31.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           385
  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"
D67V4, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED    14  39
  DEL PEAK 16(7Q31.1) WILD-TYPE 127 348
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED     14   39
  DEL PEAK 16(7Q31.1) WILD-TYPE  127  348
     clus
vv    DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  NO                           14                           127
  YES                          39                           348
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(7Q31.1) MUTATED    37   2   3   6
  DEL PEAK 16(7Q31.1) WILD-TYPE 326  21  14  29
D67V5, multiclass
    clus
vv   DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
  R0                          37                           326
  R1                           2                            21
  R2                           3                            14
  RX                           6                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(7Q31.1) MUTATED                                  0     0
  DEL PEAK 16(7Q31.1) WILD-TYPE                                4    20
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 16(7Q31.1) MUTATED                          16
  DEL PEAK 16(7Q31.1) WILD-TYPE                        85
                               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   335
D67V6, multiclass
                                           clus
vv                                          DEL PEAK 16(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               0
  BLACK OR AFRICAN AMERICAN                                          16
  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                                                                20
  BLACK OR AFRICAN AMERICAN                                            85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  WHITE                                                               335
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(7Q31.1) MUTATED     1  38
  DEL PEAK 16(7Q31.1) WILD-TYPE  13 329
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(7Q31.1) MUTATED      1   38
  DEL PEAK 16(7Q31.1) WILD-TYPE   13  329
                        clus
vv                       DEL PEAK 16(7Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       DEL PEAK 16(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           329
[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    47  15
  DEL PEAK 17(7Q36.1) WILD-TYPE 410  54
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           62                           464 
  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                           15                            54 
$`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 
       14.43        34.16        10.19         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        46.78        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 
       22.06        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 
      110.10        48.36        51.42        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        10.19        20.05        45.76        11.38        96.69 
TCGA-FI-A2EW TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KP-A3W3 TCGA-PG-A5BC 
       59.01        29.23        41.06        45.01        26.10        23.24 
TCGA-PG-A7D5 TCGA-PG-A915 
       23.97         7.00 

$`DEL PEAK 17(7Q36.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R7 
       36.82        28.27        20.81        23.21        68.65        17.59 
TCGA-A5-A0R8 TCGA-A5-A0R9 TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF 
       19.59        24.62        29.06        42.35        15.95         7.92 
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        10.26         0.39        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36         1.12         0.76        18.90         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        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        63.91        45.53        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LI 
       20.91        48.79       117.99       110.37        63.16        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-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-AP-A5FX TCGA-AW-A1PO 
       10.42        27.85        16.24        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        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-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        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.56        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI 
        0.26         0.30         1.18        18.35        14.47         0.39 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        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        27.29 
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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       33.11        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        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-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-A222 TCGA-BG-A2AD 
       14.01        15.45        15.45        14.27         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
        0.72        16.87        18.02        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
        3.52        41.42         8.48         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       24.30        12.39        31.10        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 
        6.67        27.32        16.04         7.36        16.80        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       49.15        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       27.16        17.88        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-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 
       11.08         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-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       14.14        19.89        14.70        16.96         5.88        40.01 
TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       41.06        39.88        39.95         7.99        13.84         8.98 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI 
        9.07        28.93        28.96        25.02         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 
       14.04         2.43        23.74        13.28         9.47        18.21 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE 
                         1.18                          0.07 
  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 
                        22.16                         23.47 
[1] "1.2 - 125.4 (22.2)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.1"
D68V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 17(7Q36.1) MUTATED                                        12
  DEL PEAK 17(7Q36.1) WILD-TYPE                                     383
                               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                                  46
  DEL PEAK 17(7Q36.1) WILD-TYPE                                66
D68V3, multiclass
                                         clus
vv                                        DEL PEAK 17(7Q36.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          12
  MIXED SEROUS AND ENDOMETRIOID                                     4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                46
                                         clus
vv                                        DEL PEAK 17(7Q36.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           383
  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"
D68V4, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED    18  44
  DEL PEAK 17(7Q36.1) WILD-TYPE 123 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED     18   44
  DEL PEAK 17(7Q36.1) WILD-TYPE  123  343
     clus
vv    DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  NO                           18                           123
  YES                          44                           343
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(7Q36.1) MUTATED    44   2   4   6
  DEL PEAK 17(7Q36.1) WILD-TYPE 319  21  13  29
D68V5, multiclass
    clus
vv   DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
  R0                          44                           319
  R1                           2                            21
  R2                           4                            13
  RX                           6                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q36.1) MUTATED                                  0     2
  DEL PEAK 17(7Q36.1) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 17(7Q36.1) MUTATED                          17
  DEL PEAK 17(7Q36.1) WILD-TYPE                        84
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 17(7Q36.1) MUTATED                                           1    37
  DEL PEAK 17(7Q36.1) WILD-TYPE                                         8   329
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                                                              37
                                           clus
vv                                          DEL PEAK 17(7Q36.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            84
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  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"
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q36.1) MUTATED     1  45
  DEL PEAK 17(7Q36.1) WILD-TYPE  13 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q36.1) MUTATED      1   45
  DEL PEAK 17(7Q36.1) WILD-TYPE   13  322
                        clus
vv                       DEL PEAK 17(7Q36.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       DEL PEAK 17(7Q36.1) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           322
[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    87  26
  DEL PEAK 18(8P23.2) WILD-TYPE 370  43
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          113                           413 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           26                            43 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 
       41.06        36.69        65.75        11.44        36.33        46.32 
TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3QS 
       28.64         1.18        14.43        20.81        21.21        16.87 
TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 
       16.87        57.80        45.53        36.89        48.79       125.42 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW 
        3.39        97.71        46.78        21.90         0.56        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       16.96        20.28        12.43        25.12        36.39         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A3FX TCGA-AX-A3G3 
       30.12        71.24        19.36        17.75        43.82         1.38 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.30         0.39        80.38        27.29        17.85         4.11 
TCGA-B5-A11I TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
       75.72       191.84       102.31        11.87        12.79        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0YU 
       34.13        34.95        22.06        36.49        21.17        14.83 
TCGA-BG-A2AE TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 
       23.70         6.81        10.16        24.13        61.87        67.20 
TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S 
       29.95        22.55        39.48        27.42        11.51        18.67 
TCGA-D1-A16V TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN 
        3.95        13.22         0.72        44.88         4.11        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y7 TCGA-EO-A22X TCGA-EO-A2CG 
        9.37        12.39       110.10        49.15        57.60        51.42 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A1GV 
       34.39        27.16        22.26        23.90        15.09        15.81 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       10.19        14.40        20.05        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2D2 TCGA-FI-A2EU 
       11.38        17.92        14.70         5.88        39.95        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       59.01         9.07        28.93        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 
        7.76        14.04        23.74        13.28         9.47        18.21 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       23.24        23.97        12.92         7.00         4.44 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.16         1.12         0.76        18.90         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        17.06        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV 
       15.62        10.19        15.35        15.95        14.76        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 
       12.82        20.78         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-A05N 
        5.95        23.31        86.07         8.22        63.91        23.87 
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-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        36.13        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-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CE 
       65.88        13.28        19.20        13.55        15.25        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H7 
       76.83        72.56        54.12        67.50        11.08        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HJ 
       61.18        81.37        34.32        46.49        26.33        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
        2.96        31.13        64.93         0.23         0.20         0.56 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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-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-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-A1MU TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57        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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        14.27        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        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-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-A0VZ TCGA-BG-A0W1 TCGA-BG-A0W2 TCGA-BG-A0YV 
       16.34        34.29        52.64        52.83        56.58        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-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 
        1.81         9.57        20.02        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         6.21        10.22        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        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-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-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        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY 
       24.30         2.33        22.92         1.41        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DF-A2KV 
       41.42         8.48         0.26         4.27        16.93        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-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 
       27.32        16.04         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 
       61.74        61.55        66.90        46.26        51.52        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       26.43        35.15        17.19        17.88        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
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-A1GT 
        6.90        19.27        18.84        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A215 
       12.43        11.08         6.48        19.33        12.59        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        14.14        19.89        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       40.01        41.06        39.88         7.99        13.84         8.98 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-KJ-A3U4 TCGA-KP-A3W3 TCGA-PG-A6IB 
       28.96        25.02        29.23         2.43        26.10        15.45 
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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         0.30                          0.07 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       191.84                        185.79 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        22.26                         23.47 
[1] "0.3 - 191.8 (22.3)" "0.1 - 185.8 (23.5)"
[1] "hr=" "2.3"
D69V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                        34
  DEL PEAK 18(8P23.2) WILD-TYPE                                     361
                               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                                  76
  DEL PEAK 18(8P23.2) WILD-TYPE                                36
D69V3, multiclass
                                         clus
vv                                        DEL PEAK 18(8P23.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          34
  MIXED SEROUS AND ENDOMETRIOID                                     5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                76
                                         clus
vv                                        DEL PEAK 18(8P23.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           361
  MIXED SEROUS AND ENDOMETRIOID                                      16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V4, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED    24  91
  DEL PEAK 18(8P23.2) WILD-TYPE 117 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED     24   91
  DEL PEAK 18(8P23.2) WILD-TYPE  117  296
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                           24                           117
  YES                          91                           296
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED    69   5   7  11
  DEL PEAK 18(8P23.2) WILD-TYPE 294  18  10  24
D69V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                          69                           294
  R1                           5                            18
  R2                           7                            10
  RX                          11                            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 18(8P23.2) MUTATED                                  1     2
  DEL PEAK 18(8P23.2) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 18(8P23.2) MUTATED                          35
  DEL PEAK 18(8P23.2) WILD-TYPE                        66
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 18(8P23.2) MUTATED                                           2    67
  DEL PEAK 18(8P23.2) WILD-TYPE                                         7   299
D69V6, multiclass
                                           clus
vv                                          DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          35
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              67
                                           clus
vv                                          DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             7
  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"
D69V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     1  82
  DEL PEAK 18(8P23.2) WILD-TYPE  13 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      1   82
  DEL PEAK 18(8P23.2) WILD-TYPE   13  285
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          82
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                13
  NOT HISPANIC OR LATINO                           285
[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    88  24
  DEL PEAK 19(8P21.2) WILD-TYPE 369  45
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                          112                           414 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                           24                            45 
$`DEL PEAK 19(8P21.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 
       41.06        36.69        65.75        11.44        36.33        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3IA TCGA-AJ-A3NF 
       46.32        28.64         1.18        14.43        20.81        21.21 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
       16.87        16.87        57.80        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AW-A1PO 
      125.42         3.39        97.71        46.78        21.90         0.56 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CN 
       37.78        16.96        13.55        20.28        12.43        25.12 
TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A3G3 
       36.39         4.77        30.12        71.24        19.36         1.38 
TCGA-AX-A3G4 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.30         0.39        80.38        27.29        17.85         4.11 
TCGA-B5-A11I TCGA-B5-A1MR TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 
       75.72       191.84       102.31        11.87        12.79        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A2AE 
       34.13        34.95        22.06        36.49        21.17        23.70 
TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A0ZP 
        6.81        10.16        24.13        61.87        67.20        29.95 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A179 
       22.55        39.48        27.42        11.51        18.67        14.73 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A2QT 
       13.22         0.72        44.88         4.11        35.38        12.39 
TCGA-DI-A2QY TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3AS TCGA-EO-A3AZ 
      110.10        37.71        57.60        51.42        34.39        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A212 
       26.96        22.26        23.90        15.09        15.81        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       14.40        20.05        29.10        27.35        13.84        11.38 
TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW 
       17.92         5.88        41.06        39.95        96.69        59.01 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
        9.07        28.93        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC 
       14.04        23.74        13.28         9.47        18.21        23.24 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 
       23.97        12.92         7.00         4.44 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         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        17.06        36.99        20.65        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       10.19        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         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        63.91        23.87        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        36.13        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-A1C9 TCGA-AX-A1CE TCGA-AX-A1CF TCGA-AX-A1CI 
       13.28        19.20        15.25        20.05        76.83        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       54.12        67.50        11.08        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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-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-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-A1MU TCGA-B5-A1MV 
       19.50        18.41        17.36        16.57        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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        33.11        14.27        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        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-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-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-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B TCGA-BK-A13C 
       35.90        34.98         6.21        10.22        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-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-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-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-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-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.79        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-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-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-A3DA TCGA-D1-A3DG TCGA-D1-A3JP 
        3.52        41.42         8.48         0.26         4.27        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-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        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        49.15        61.74        61.55        66.90        46.26 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       51.52        19.40        26.43        35.15        17.19        17.88 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       16.34        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK 
       53.88        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-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       16.11        12.43        11.08         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 
       18.87        22.82        45.76        31.04        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
       14.70        16.96        40.01        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-KJ-A3U4 TCGA-KP-A3W3 
        8.98        28.96        25.02        29.23         2.43        26.10 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                         0.30                          0.07 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                       191.84                        185.79 
  DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE 
                        23.47                         23.34 
[1] "0.3 - 191.8 (23.5)" "0.1 - 185.8 (23.3)"
[1] "hr=" "2"  
D70V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 19(8P21.2) MUTATED                                        26
  DEL PEAK 19(8P21.2) WILD-TYPE                                     369
                               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                                  81
  DEL PEAK 19(8P21.2) WILD-TYPE                                31
D70V3, multiclass
                                         clus
vv                                        DEL PEAK 19(8P21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          26
  MIXED SEROUS AND ENDOMETRIOID                                     6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                81
                                         clus
vv                                        DEL PEAK 19(8P21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           369
  MIXED SEROUS AND ENDOMETRIOID                                      15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V4, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P21.2) MUTATED    24  89
  DEL PEAK 19(8P21.2) WILD-TYPE 117 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P21.2) MUTATED     24   89
  DEL PEAK 19(8P21.2) WILD-TYPE  117  298
     clus
vv    DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE
  NO                           24                           117
  YES                          89                           298
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P21.2) MUTATED    70   5   7   9
  DEL PEAK 19(8P21.2) WILD-TYPE 293  18  10  26
D70V5, multiclass
    clus
vv   DEL PEAK 19(8P21.2) MUTATED DEL PEAK 19(8P21.2) WILD-TYPE
  R0                          70                           293
  R1                           5                            18
  R2                           7                            10
  RX                           9                            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 19(8P21.2) MUTATED                                  1     2
  DEL PEAK 19(8P21.2) WILD-TYPE                                3    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 19(8P21.2) MUTATED                          34
  DEL PEAK 19(8P21.2) WILD-TYPE                        67
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 19(8P21.2) MUTATED                                           2    65
  DEL PEAK 19(8P21.2) WILD-TYPE                                         7   301
D70V6, multiclass
                                           clus
vv                                          DEL PEAK 19(8P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              65
                                           clus
vv                                          DEL PEAK 19(8P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                18
  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"
D70V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P21.2) MUTATED     2  78
  DEL PEAK 19(8P21.2) WILD-TYPE  12 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P21.2) MUTATED      2   78
  DEL PEAK 19(8P21.2) WILD-TYPE   12  289
                        clus
vv                       DEL PEAK 19(8P21.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          78
                        clus
vv                       DEL PEAK 19(8P21.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           289
[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    59  17
  DEL PEAK 20(9P23) WILD-TYPE 398  52
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         76                         450 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                         17                          52 
$`DEL PEAK 20(9P23) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       36.69       149.56        87.32        36.82        19.96        17.59 
TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N 
       42.35        36.33        28.64         7.33         1.18        14.43 
TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3IA 
       34.16         1.12        18.90         1.64        17.06        20.81 
TCGA-AJ-A3NH TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AP-A1DQ 
       10.19        20.78        45.53        48.79        97.71        46.78 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF 
       21.90         0.56        37.78        16.96        13.55        76.83 
TCGA-AX-A2H2 TCGA-AX-A3FX TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-B5-A0K8 TCGA-B5-A0KB 
        4.77        43.82         0.30         0.26        17.85         4.11 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M8 
       36.82       102.31       116.25        33.11        34.95        36.49 
TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V 
       15.45        10.16        16.64        49.55        22.55        39.48 
TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A1O0 TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QT 
       37.32        18.67         2.07        16.93        35.38        12.39 
TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 
      110.10        27.32        49.15        51.42        27.16        26.96 
TCGA-EY-A1GO TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D 
       19.27        15.09        14.40        11.38        14.70         5.88 
TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       39.95         9.07        28.93         7.76        14.04         9.47 
TCGA-KP-A3W3 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QS-A8F1 
       26.10        23.24        23.97         4.44 

$`DEL PEAK 20(9P23) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88        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       112.54       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-A2K2 TCGA-A5-A2K3 
        7.92        11.44         9.60         8.02        91.04        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LP TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        5.33         5.16        14.96        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
       29.39         2.40        34.36         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG 
       22.49        22.26        36.99        20.65        21.21        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       12.82         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        63.91        57.80        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE 
       23.87        12.20        20.91       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-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        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-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-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO 
       26.33        17.75        30.74         2.96        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.23         0.20         0.56         0.20        20.52         1.38 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN 
        0.30         1.18        18.35        14.47         0.39        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        27.29 
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-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-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-A1N2 
       14.40        14.70        11.70        11.87        15.29        12.79 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       34.98        22.06        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        20.02        23.70        20.12        11.31         6.81 
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-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-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-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         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K 
        7.00         0.99        30.44         1.28        28.01        28.08 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S 
       26.37        10.22         1.51         1.78        11.15        24.30 
TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        2.33        22.92         1.41        13.22         0.72        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-D1-A3DH 
       41.42         8.48        44.88         0.26         4.27         4.11 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 
       24.30         9.37        31.10        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        16.04         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        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        22.26        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        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-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW 
       17.88        17.62        16.11        12.43        15.81        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM 
        6.48        19.33        12.59        10.19        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       20.05        45.76        31.04        29.10        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92        14.14        19.89        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.88         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.96        25.02        29.23        41.06        45.01         1.74 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
        2.43        23.74        13.28        18.21        15.45        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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                       0.26                        0.07 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                     149.56                      191.84 
  DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE 
                     21.355                      23.470 
[1] "0.3 - 149.6 (21.4)" "0.1 - 191.8 (23.5)"
[1] "hr=" "1.9"
D71V2, continuous
                             vv
clus                          ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 20(9P23) MUTATED                                        28
  DEL PEAK 20(9P23) WILD-TYPE                                     367
                             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                                  44
  DEL PEAK 20(9P23) WILD-TYPE                                68
D71V3, multiclass
                                         clus
vv                                        DEL PEAK 20(9P23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                        28
  MIXED SEROUS AND ENDOMETRIOID                                   4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                              44
                                         clus
vv                                        DEL PEAK 20(9P23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         367
  MIXED SEROUS AND ENDOMETRIOID                                    17
  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"
D71V4, binary
                             cls
clus                            0   1
  DEL PEAK 20(9P23) MUTATED    13  63
  DEL PEAK 20(9P23) WILD-TYPE 128 324
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(9P23) MUTATED     13   63
  DEL PEAK 20(9P23) WILD-TYPE  128  324
     clus
vv    DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  NO                         13                         128
  YES                        63                         324
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(9P23) MUTATED    49   3   5   5
  DEL PEAK 20(9P23) WILD-TYPE 314  20  12  30
D71V5, multiclass
    clus
vv   DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  R0                        49                         314
  R1                         3                          20
  R2                         5                          12
  RX                         5                          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
  DEL PEAK 20(9P23) MUTATED                                  1     2
  DEL PEAK 20(9P23) WILD-TYPE                                3    18
                             vv
clus                          BLACK OR AFRICAN AMERICAN
  DEL PEAK 20(9P23) MUTATED                          21
  DEL PEAK 20(9P23) WILD-TYPE                        80
                             vv
clus                          NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 20(9P23) MUTATED                                           2    45
  DEL PEAK 20(9P23) WILD-TYPE                                         7   321
D71V6, multiclass
                                           clus
vv                                          DEL PEAK 20(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                  1
  ASIAN                                                             2
  BLACK OR AFRICAN AMERICAN                                        21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                         2
  WHITE                                                            45
                                           clus
vv                                          DEL PEAK 20(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                    3
  ASIAN                                                              18
  BLACK OR AFRICAN AMERICAN                                          80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           7
  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"
D71V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(9P23) MUTATED     1  55
  DEL PEAK 20(9P23) WILD-TYPE  13 312
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(9P23) MUTATED      1   55
  DEL PEAK 20(9P23) WILD-TYPE   13  312
                        clus
vv                       DEL PEAK 20(9P23) MUTATED DEL PEAK 20(9P23) WILD-TYPE
  HISPANIC OR LATINO                             1                          13
  NOT HISPANIC OR LATINO                        55                         312
[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    95  31
  DEL PEAK 21(9Q21.2) WILD-TYPE 362  38
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                          126                           400 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                           31                            38 
$`DEL PEAK 21(9Q21.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       41.06        36.69        87.32        36.82        19.96        17.59 
TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       42.35        36.33        91.04        28.64         7.33         1.18 
TCGA-AJ-A2QK TCGA-AJ-A2QN TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        0.39         2.40        34.16         1.12        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU 
       22.26        17.06        20.81        10.19        16.87        20.78 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 
       21.99         5.95        57.80        45.53        48.79       125.42 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IW 
       97.71        46.78        21.90        36.13        53.92        37.78 
TCGA-AX-A1C7 TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 
       16.96        76.83        36.39        11.08        30.12        61.18 
TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       19.36         2.96         0.23        43.82        20.52         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I 
        0.26         0.39        80.38        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-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV 
       33.11        29.65        34.95        22.06        36.49        12.56 
TCGA-BG-A18C TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD 
       15.45         1.81        10.22        10.16        24.13        16.64 
TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 
       61.87        49.55         8.55        22.55        39.48        37.32 
TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW 
       31.07        18.67         3.95        28.08        13.22         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT 
        2.07         4.11        16.93        35.38         9.37        12.39 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG 
      110.10        48.36        27.32        49.15        37.71        51.42 
TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO 
       19.40        27.16        26.96        16.34         4.54        19.27 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON 
       15.81        11.08        12.59        10.19        14.40        20.05 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EY 
       29.10        11.38        17.92        41.06        39.95        28.93 
TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ 
       25.02        41.06        45.01         7.76        14.04        23.74 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A914 TCGA-QS-A8F1 TCGA-SL-A6J9 
       26.10        18.21        23.24        12.92         4.44         0.07 

$`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 
       10.29       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       112.54       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        14.43        10.26        19.79        29.39 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       34.36         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        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87        22.32        12.82         2.70         0.13        83.67 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05J TCGA-AP-A05N 
       23.31        86.07         8.22        63.91        36.89        23.87 
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-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        40.80        81.37        34.32        46.49 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FT 
       26.33        17.75        30.74        31.13        64.93         0.20 
TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.56         0.20         1.38         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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 
       27.29        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-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        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-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-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 
       20.02        23.70        20.12        11.31         6.81        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
       34.98         6.21        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-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU TCGA-D1-A0ZV 
       19.79        29.95         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-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.27        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        31.10        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R 
        6.67        16.04         7.36        16.80        10.92        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        51.52        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX 
       26.43        35.15        17.19        17.88        22.26        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        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-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
       18.84        17.88        17.62        15.09        16.11        12.43 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP 
        6.48        19.33        18.87        22.82        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        13.84        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.88        40.01        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-H5-A2HR 
       96.69        59.01         9.07        28.96        29.23         1.74 
TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 
        2.43        13.28         9.47        15.45        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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        14.07        18.28         0.23 

  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                         0.07                          0.13 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE 
                       21.945                        23.670 
[1] "0.1 - 125.4 (21.9)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.7"
D72V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 21(9Q21.2) MUTATED                                        49
  DEL PEAK 21(9Q21.2) WILD-TYPE                                     346
                               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                                  67
  DEL PEAK 21(9Q21.2) WILD-TYPE                                45
D72V3, multiclass
                                         clus
vv                                        DEL PEAK 21(9Q21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          49
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                67
                                         clus
vv                                        DEL PEAK 21(9Q21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           346
  MIXED SEROUS AND ENDOMETRIOID                                      11
  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"
D72V4, binary
                               cls
clus                              0   1
  DEL PEAK 21(9Q21.2) MUTATED    27  99
  DEL PEAK 21(9Q21.2) WILD-TYPE 114 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9Q21.2) MUTATED     27   99
  DEL PEAK 21(9Q21.2) WILD-TYPE  114  288
     clus
vv    DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE
  NO                           27                           114
  YES                          99                           288
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(9Q21.2) MUTATED    79   5   7  11
  DEL PEAK 21(9Q21.2) WILD-TYPE 284  18  10  24
D72V5, multiclass
    clus
vv   DEL PEAK 21(9Q21.2) MUTATED DEL PEAK 21(9Q21.2) WILD-TYPE
  R0                          79                           284
  R1                           5                            18
  R2                           7                            10
  RX                          11                            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 21(9Q21.2) MUTATED                                  1     1
  DEL PEAK 21(9Q21.2) WILD-TYPE                                3    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 21(9Q21.2) MUTATED                          34
  DEL PEAK 21(9Q21.2) WILD-TYPE                        67
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 21(9Q21.2) MUTATED                                           2    81
  DEL PEAK 21(9Q21.2) WILD-TYPE                                         7   285
D72V6, multiclass
                                           clus
vv                                          DEL PEAK 21(9Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          34
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           2
  WHITE                                                              81
                                           clus
vv                                          DEL PEAK 21(9Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            67
  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"
D72V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(9Q21.2) MUTATED     4  88
  DEL PEAK 21(9Q21.2) WILD-TYPE  10 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9Q21.2) MUTATED      4   88
  DEL PEAK 21(9Q21.2) WILD-TYPE   10  279
                        clus
vv                       DEL PEAK 21(9Q21.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       DEL PEAK 21(9Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           279
[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    97  30
  DEL PEAK 22(9Q34.2) WILD-TYPE 360  39
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                          127                           399 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                           30                            39 
$`DEL PEAK 22(9Q34.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GR TCGA-A5-A0R6 
       41.06        36.69        87.32        65.75        36.82        19.96 
TCGA-A5-A0R7 TCGA-A5-A0VP TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO 
       17.59        42.35        11.44        91.04        28.64         7.33 
TCGA-AJ-A23M TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        1.18         0.39        34.16         1.12        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A6NU TCGA-AP-A052 
       22.26        17.06        20.81        10.19        20.78        21.99 
TCGA-AP-A053 TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
        5.95        45.53        36.89        48.79       125.42        97.71 
TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A0IW TCGA-AX-A1C7 
       21.90        36.13         0.56        53.92        37.78        16.96 
TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF 
       76.83        36.39        11.08        30.12        61.18        19.36 
TCGA-AX-A3FS TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
        0.23        43.82        20.52         0.30         0.26         0.39 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11H TCGA-B5-A11P 
       80.38        27.29        17.85         4.11        88.34        36.82 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
      102.31        50.89        11.87       116.25        33.11        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C 
       34.13        34.95        22.06        36.49        12.56        15.45 
TCGA-BG-A221 TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A26L TCGA-BS-A0TI TCGA-BS-A0U9 
        1.81        10.22        10.16        24.13        61.87        67.20 
TCGA-BS-A0V8 TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N 
       49.55         8.55        22.55        39.48        37.32        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 
       18.67         3.95        28.08        13.22         0.72         2.07 
TCGA-D1-A2G7 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU 
       44.88         4.11        16.93        35.38         9.37        31.10 
TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
      110.10        48.36        27.32        10.92        49.15        37.71 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A1GC 
       51.42        19.40        27.16        26.96        16.34         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A212 
       23.90         6.90        17.62        15.81        11.08        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-FI-A2CY TCGA-FI-A2D2 
       14.40        20.05        29.10        11.38        41.06        39.95 
TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        9.07        28.93        25.02        29.23        41.06        45.01 
TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
       14.04        23.74         9.47        26.10        18.21        23.24 
TCGA-QS-A8F1 
        4.44 

$`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 
       10.29       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       112.54       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        14.43        10.26        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       34.36         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        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        16.87        22.32        12.82         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05D 
       83.67        23.31        86.07         8.22        63.91        57.80 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        12.20        20.91       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        46.78 
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-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-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-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       20.28        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12         4.77        71.24        40.80        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       46.49        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G7 
       64.93         0.20         0.56         0.20         1.38         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        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-A11I TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        75.72        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-A1N2 TCGA-B5-A3FA 
       14.40        14.70        11.70        15.29        12.79        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        14.27        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        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-A222 TCGA-BG-A2AD TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        9.57        20.02        23.70        20.12        11.31         6.81 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       35.90        34.98         6.21        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        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-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       16.83        19.79        29.95         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-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I 
       36.10        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 
       22.92         1.41        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-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.27        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 
       36.62        24.30        12.39        23.38        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S 
        6.67        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU 
       66.90        46.26        57.60        51.52        34.39        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 
       35.15        17.19        17.88        22.26        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.34        22.78        13.97        19.27        18.84        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-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       18.87        22.82        45.76        31.04        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D 
       17.92        14.14        19.89        14.70        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W0 
       59.01        28.96         1.74         7.76         2.43        13.28 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 
       15.45        23.97        12.92         7.00        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       18.28         0.07         0.23 

  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                         0.23                          0.07 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                       125.42                        191.84 
  DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE 
                        23.74                         23.34 
[1] "0.2 - 125.4 (23.7)" "0.1 - 191.8 (23.3)"
[1] "hr=" "2.5"
D73V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 22(9Q34.2) MUTATED                                        52
  DEL PEAK 22(9Q34.2) WILD-TYPE                                     343
                               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                                  66
  DEL PEAK 22(9Q34.2) WILD-TYPE                                46
D73V3, multiclass
                                         clus
vv                                        DEL PEAK 22(9Q34.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          52
  MIXED SEROUS AND ENDOMETRIOID                                    10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                66
                                         clus
vv                                        DEL PEAK 22(9Q34.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           343
  MIXED SEROUS AND ENDOMETRIOID                                      11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.2) MUTATED    27 101
  DEL PEAK 22(9Q34.2) WILD-TYPE 114 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.2) MUTATED     27  101
  DEL PEAK 22(9Q34.2) WILD-TYPE  114  286
     clus
vv    DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE
  NO                           27                           114
  YES                         101                           286
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9Q34.2) MUTATED    79   5   6  12
  DEL PEAK 22(9Q34.2) WILD-TYPE 284  18  11  23
D73V5, multiclass
    clus
vv   DEL PEAK 22(9Q34.2) MUTATED DEL PEAK 22(9Q34.2) WILD-TYPE
  R0                          79                           284
  R1                           5                            18
  R2                           6                            11
  RX                          12                            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 22(9Q34.2) MUTATED                                  0     2
  DEL PEAK 22(9Q34.2) WILD-TYPE                                4    18
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 22(9Q34.2) MUTATED                          31
  DEL PEAK 22(9Q34.2) WILD-TYPE                        70
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 22(9Q34.2) MUTATED                                           3    83
  DEL PEAK 22(9Q34.2) WILD-TYPE                                         6   283
D73V6, multiclass
                                           clus
vv                                          DEL PEAK 22(9Q34.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    0
  ASIAN                                                               2
  BLACK OR AFRICAN AMERICAN                                          31
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           3
  WHITE                                                              83
                                           clus
vv                                          DEL PEAK 22(9Q34.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      4
  ASIAN                                                                18
  BLACK OR AFRICAN AMERICAN                                            70
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             6
  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"
D73V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9Q34.2) MUTATED     3  91
  DEL PEAK 22(9Q34.2) WILD-TYPE  11 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9Q34.2) MUTATED      3   91
  DEL PEAK 22(9Q34.2) WILD-TYPE   11  276
                        clus
vv                       DEL PEAK 22(9Q34.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       DEL PEAK 22(9Q34.2) WILD-TYPE
  HISPANIC OR LATINO                                11
  NOT HISPANIC OR LATINO                           276
[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    58  16
  DEL PEAK 23(10Q23.31) WILD-TYPE 399  53
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             74                             452 
  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                             16                              53 
$`DEL PEAK 23(10Q23.31) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A3LP 
       41.06        87.32        65.75        11.44        36.33        14.96 
TCGA-AJ-A2QM TCGA-AJ-A3BF TCGA-AJ-A3EM TCGA-AJ-A3IA TCGA-AJ-A3TW TCGA-AP-A052 
       29.39         1.12        22.26        20.81        16.87        21.99 
TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1CR 
      125.42         3.39        36.13         0.56        53.92        11.08 
TCGA-AX-A2HK TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
        2.96        20.52         1.38         0.30         0.26         0.39 
TCGA-B5-A0JN TCGA-B5-A0K2 TCGA-B5-A0K3 TCGA-B5-A0KB TCGA-B5-A1MS TCGA-B5-A3FD 
       80.38        25.91        27.29         4.11       102.31        33.11 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0TE TCGA-BS-A0U9 TCGA-D1-A160 
       36.49        15.45         6.81         4.80        67.20         3.68 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A1NU 
       11.51        29.92        31.07        28.01        28.08        13.22 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QY 
        2.07         4.27         4.11        16.93        35.38       110.10 
TCGA-EO-A1Y5 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 
       10.92        51.42        19.40        34.39        27.16        26.96 
TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
       16.34        23.90         6.90        17.62        15.09        11.08 
TCGA-EY-A214 TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2F8 
       14.40        27.35        11.38        39.95        96.69        25.02 
TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W3 TCGA-KP-A3W4 
       41.06         7.76        14.04         2.43        26.10        18.21 
TCGA-PG-A914 TCGA-QS-A8F1 
       12.92         4.44 

$`DEL PEAK 23(10Q23.31) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54       105.37        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-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
        7.33         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK 
        2.40        34.36        34.16         0.76        18.90         1.68 
TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE 
        1.64        14.66        22.49        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       21.21        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         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        63.91 
TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       57.80        45.53        36.89        23.87        12.20        20.91 
TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LI 
       48.79       117.99       110.37        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        46.78        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        21.90        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-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-A2H4 
       54.12        67.50        25.12        36.39         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO 
       19.36        26.33        17.75        30.74        31.13        64.93 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 
        0.23         0.20         0.56        43.82         0.20         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        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-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 
       30.51        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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       22.06        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-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 
       20.02        23.70        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-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-A15V TCGA-D1-A15W TCGA-D1-A15X TCGA-D1-A15Z 
        4.44        21.99        39.48        30.08        29.88         1.91 
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-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        0.99        30.44         1.28        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-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-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       24.30         9.37        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        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        51.52        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.88        22.26        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        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-A212 
       12.43        15.81         6.48        19.33        12.59        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A2OQ 
       18.87        22.82        20.05        45.76        31.04        29.10 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       13.84        17.92        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
        5.88        40.01        41.06        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F9 
        8.98        59.01         9.07        28.93        28.96        29.23 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC 
       45.01         1.74        23.74        13.28         9.47        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       15.45        23.97         7.00        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE 
                           0.26                            0.07 
  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 
                         18.805                          23.670 
[1] "0.3 - 125.4 (18.8)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.2"
D74V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 23(10Q23.31) MUTATED                                        31
  DEL PEAK 23(10Q23.31) WILD-TYPE                                     364
                                 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                                  39
  DEL PEAK 23(10Q23.31) WILD-TYPE                                73
D74V3, multiclass
                                         clus
vv                                        DEL PEAK 23(10Q23.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            31
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  39
                                         clus
vv                                        DEL PEAK 23(10Q23.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             364
  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"
D74V4, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10Q23.31) MUTATED    10  65
  DEL PEAK 23(10Q23.31) WILD-TYPE 131 322
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q23.31) MUTATED     10   65
  DEL PEAK 23(10Q23.31) WILD-TYPE  131  322
     clus
vv    DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  NO                             10                             131
  YES                            65                             322
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 23(10Q23.31) MUTATED    47   2   5   6
  DEL PEAK 23(10Q23.31) WILD-TYPE 316  21  12  29
D74V5, multiclass
    clus
vv   DEL PEAK 23(10Q23.31) MUTATED DEL PEAK 23(10Q23.31) WILD-TYPE
  R0                            47                             316
  R1                             2                              21
  R2                             5                              12
  RX                             6                              29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10Q23.31) MUTATED                                  0     3
  DEL PEAK 23(10Q23.31) WILD-TYPE                                4    17
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 23(10Q23.31) MUTATED                          19
  DEL PEAK 23(10Q23.31) WILD-TYPE                        82
                                 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      44
  DEL PEAK 23(10Q23.31) WILD-TYPE   322
D74V6, multiclass
                                           clus
vv                                          DEL PEAK 23(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 3
  BLACK OR AFRICAN AMERICAN                                            19
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                                44
                                           clus
vv                                          DEL PEAK 23(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  17
  BLACK OR AFRICAN AMERICAN                                              82
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               7
  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"
D74V7, binary
                                 cls
clus                                0   1
  DEL PEAK 23(10Q23.31) MUTATED     2  53
  DEL PEAK 23(10Q23.31) WILD-TYPE  12 314
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 23(10Q23.31) MUTATED      2   53
  DEL PEAK 23(10Q23.31) WILD-TYPE   12  314
                        clus
vv                       DEL PEAK 23(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 23(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  12
  NOT HISPANIC OR LATINO                             314
[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    81  20
  DEL PEAK 24(11P15.5) WILD-TYPE 376  49
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                           101                            425 
  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                            20                             49 
$`DEL PEAK 24(11P15.5) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A1OG 
       41.06        36.69       149.56        65.75        60.53        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LP TCGA-AJ-A23M 
       36.33        91.04        46.32        28.64        14.96         1.18 
TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
        0.39        34.16         1.12        18.90         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AP-A05A TCGA-AP-A0LF TCGA-AP-A0LI 
       20.81        21.21        10.19        63.91         3.39        97.71 
TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1CA TCGA-AX-A1CF 
       46.78        21.90        37.78        16.96        20.28        76.83 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A3FW TCGA-AX-A3G1 TCGA-AX-A3G3 
       11.08         4.77        30.12         0.56        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.30         0.26         0.39        80.38        17.85         4.11 
TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD 
       36.82       102.31        12.79       116.25        33.11        34.13 
TCGA-B5-A5OE TCGA-BG-A0MC TCGA-BG-A0YV TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD 
       34.95        41.52        12.56        10.22        10.16        16.64 
TCGA-BS-A0TI TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A17K 
       61.87        39.48        37.32        11.51        18.67        28.08 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP 
        0.72        18.25         2.07         4.27         4.11        16.93 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 
        9.37        12.39        31.10       110.10        48.36        27.32 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3B1 TCGA-EY-A1GJ 
       37.71        51.42        19.40        34.39        26.96        23.90 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO 
       19.27        18.84        15.09        10.19        14.40        45.76 
TCGA-EY-A2OQ TCGA-EY-A54A TCGA-FI-A2D2 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
       29.10        14.70        39.95        59.01         9.07        28.93 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06         1.74         7.76        14.04         2.43        23.74 
TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-SL-A6J9 
        9.47        23.24        23.97         7.00         0.07 

$`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 
       10.29       106.88        37.02        83.51        17.85        32.78 
TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
      112.54       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        14.43        10.26        19.79        29.39 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40        34.36         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 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        23.87 
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-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        36.13 
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-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-A1CP TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       67.50        25.12        36.39        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       30.74         2.96        31.13        64.93         0.23         0.20 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       43.82         0.20         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        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        27.29 
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-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-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-A3FA 
       14.40        14.70        11.70        11.87        15.29        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-BG-A0LW 
       78.81        62.14        14.27        29.65        41.06        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        22.06 
TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MG TCGA-BG-A0MI 
       38.37        36.49        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-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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        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-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-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-A16B TCGA-D1-A16D TCGA-D1-A16E 
        0.66        15.72        36.10        36.36        37.51        36.79 
TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       27.42        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       16.87        18.02        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KV TCGA-DF-A2KY 
       41.42         8.48        44.88         0.26        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-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        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        10.92        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        51.52        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        17.88        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        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-A1GR TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX 
       17.62        16.11        12.43        15.81        11.08         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        20.05        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 
       27.35        13.84        11.38        17.92        14.14        19.89 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         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        29.23 
TCGA-FI-A3PX TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 
       45.01        13.28        26.10        18.21        15.45        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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.23 

  DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE 
                          0.07                           0.13 
  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 
                         20.52                          23.70 
[1] "0.1 - 149.6 (20.5)" "0.1 - 191.8 (23.7)"
[1] "hr=" "1.9"
D75V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 24(11P15.5) MUTATED                                        36
  DEL PEAK 24(11P15.5) WILD-TYPE                                     359
                                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                                  61
  DEL PEAK 24(11P15.5) WILD-TYPE                                51
D75V3, multiclass
                                         clus
vv                                        DEL PEAK 24(11P15.5) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           36
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 61
                                         clus
vv                                        DEL PEAK 24(11P15.5) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            359
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V4, binary
                                cls
clus                               0   1
  DEL PEAK 24(11P15.5) MUTATED    16  86
  DEL PEAK 24(11P15.5) WILD-TYPE 125 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11P15.5) MUTATED     16   86
  DEL PEAK 24(11P15.5) WILD-TYPE  125  301
     clus
vv    DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  NO                            16                            125
  YES                           86                            301
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(11P15.5) MUTATED    63   3   7   8
  DEL PEAK 24(11P15.5) WILD-TYPE 300  20  10  27
D75V5, multiclass
    clus
vv   DEL PEAK 24(11P15.5) MUTATED DEL PEAK 24(11P15.5) WILD-TYPE
  R0                           63                            300
  R1                            3                             20
  R2                            7                             10
  RX                            8                             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 24(11P15.5) MUTATED                                  1     3
  DEL PEAK 24(11P15.5) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 24(11P15.5) MUTATED                          30
  DEL PEAK 24(11P15.5) WILD-TYPE                        71
                                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      62
  DEL PEAK 24(11P15.5) WILD-TYPE   304
D75V6, multiclass
                                           clus
vv                                          DEL PEAK 24(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                           30
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               62
                                           clus
vv                                          DEL PEAK 24(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             71
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  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"
D75V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(11P15.5) MUTATED     4  74
  DEL PEAK 24(11P15.5) WILD-TYPE  10 293
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(11P15.5) MUTATED      4   74
  DEL PEAK 24(11P15.5) WILD-TYPE   10  293
                        clus
vv                       DEL PEAK 24(11P15.5) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           74
                        clus
vv                       DEL PEAK 24(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            293
[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    58  12
  DEL PEAK 25(11Q14.1) WILD-TYPE 399  57
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            70                            456 
  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                            12                             57 
$`DEL PEAK 25(11Q14.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG TCGA-A5-A2K2 
       36.69        60.53        36.82        19.96        11.44        91.04 
TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI 
       46.32        28.64         0.39        29.39        34.16        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A0LF 
        1.64        21.21        10.19        16.87        16.87         3.39 
TCGA-AP-A3K1 TCGA-AX-A1C7 TCGA-AX-A1CR TCGA-AX-A2IO TCGA-AX-A3G6 TCGA-B5-A0K3 
       21.90        16.96        11.08        64.93         0.26        27.29 
TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD 
       17.85        36.82        32.09       116.25        33.11        34.13 
TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-D1-A0ZZ 
       22.06        12.56         6.81        10.22        24.13        22.55 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A1NN 
       37.32        11.51        18.67         4.27        16.93        35.38 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3KU 
        9.37        12.39        27.32        37.71        51.42        22.26 
TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
       23.90        19.27        18.84        17.62        15.09        11.08 
TCGA-EY-A210 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D 
       12.59        45.76        27.35        11.38        14.70         5.88 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-JU-AAVI TCGA-KJ-A3U4 
       39.95        96.69         9.07        28.93         7.76         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A915 
       23.74         9.47        26.10         7.00 

$`DEL PEAK 25(11Q14.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU 
       57.53        65.75        60.53        46.55        38.37        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-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
        8.02         5.33         5.16         7.33        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       14.43        10.26        19.79         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.76         1.68        14.66        22.49        22.26        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.81        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       14.76        22.32        12.82        20.78         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 
       63.91        57.80        45.53        36.89        23.87        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-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        46.78 
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 
       36.13         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-A1CA TCGA-AX-A1CC 
       13.28        19.20        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-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       36.39         4.77        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       30.74         2.96        31.13         0.23         0.20         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G7 
       43.82         0.20        20.52         1.38         0.30         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        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-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        17.88        13.74 
TCGA-B5-A0K7 TCGA-B5-A0K9 TCGA-B5-A0KB TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11G 
       17.10        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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       78.81        62.14        14.27        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        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-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 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-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-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-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-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY 
       22.92         1.41        13.22         0.72        18.25        16.87 
TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 
       18.02         2.07        15.06         1.05         3.95         3.52 
TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-DF-A2KV 
       41.42         8.48        44.88         0.26         4.11        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        23.38        48.36        17.06         2.37 
TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 
        6.67        16.04         7.36        16.80        10.92        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ 
       19.40        34.39        26.43        35.15        17.19        27.16 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.88        26.96        16.34        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GT 
       23.34        22.78        13.97         6.90        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 
       12.43        15.81         6.48        19.33        10.19        14.40 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       18.87        22.82        20.05        31.04        29.10        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2CY 
       17.92        14.14        19.89        16.96        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 
       39.88         7.99        13.84         8.98        59.01        28.96 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-K6-A3WQ 
       25.02        29.23        41.06        45.01         1.74        14.04 
TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 
       13.28        18.21        23.24        15.45        23.97        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        12.92        23.64 
TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83         4.44        14.07        18.28         0.07         0.23 

  DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE 
                          0.26                           0.07 
  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 
                        19.615                         23.785 
[1] "0.3 - 116.2 (19.6)" "0.1 - 191.8 (23.8)"
[1] "hr=" "1.7"
D76V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 25(11Q14.1) MUTATED                                        21
  DEL PEAK 25(11Q14.1) WILD-TYPE                                     374
                                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                                  43
  DEL PEAK 25(11Q14.1) WILD-TYPE                                69
D76V3, multiclass
                                         clus
vv                                        DEL PEAK 25(11Q14.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           21
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 43
                                         clus
vv                                        DEL PEAK 25(11Q14.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            374
  MIXED SEROUS AND ENDOMETRIOID                                       15
  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"
D76V4, binary
                                cls
clus                               0   1
  DEL PEAK 25(11Q14.1) MUTATED    12  58
  DEL PEAK 25(11Q14.1) WILD-TYPE 129 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(11Q14.1) MUTATED     12   58
  DEL PEAK 25(11Q14.1) WILD-TYPE  129  329
     clus
vv    DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE
  NO                            12                            129
  YES                           58                            329
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(11Q14.1) MUTATED    47   4   3   6
  DEL PEAK 25(11Q14.1) WILD-TYPE 316  19  14  29
D76V5, multiclass
    clus
vv   DEL PEAK 25(11Q14.1) MUTATED DEL PEAK 25(11Q14.1) WILD-TYPE
  R0                           47                            316
  R1                            4                             19
  R2                            3                             14
  RX                            6                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(11Q14.1) MUTATED                                  1     2
  DEL PEAK 25(11Q14.1) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 25(11Q14.1) MUTATED                          21
  DEL PEAK 25(11Q14.1) WILD-TYPE                        80
                                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      41
  DEL PEAK 25(11Q14.1) WILD-TYPE   325
D76V6, multiclass
                                           clus
vv                                          DEL PEAK 25(11Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               41
                                           clus
vv                                          DEL PEAK 25(11Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             80
  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"
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(11Q14.1) MUTATED     5  52
  DEL PEAK 25(11Q14.1) WILD-TYPE   9 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(11Q14.1) MUTATED      5   52
  DEL PEAK 25(11Q14.1) WILD-TYPE    9  315
                        clus
vv                       DEL PEAK 25(11Q14.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 25(11Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            315
[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    74  18
  DEL PEAK 26(11Q25) WILD-TYPE 383  51
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          92                          434 
  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                          18                           51 
$`DEL PEAK 26(11Q25) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OG 
       36.69        65.75        60.53        36.82        17.59        11.44 
TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BI 
       91.04        46.32        28.64        29.39        34.16        18.90 
TCGA-AJ-A3EJ TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A052 
        1.64        20.81        10.19        16.87        16.87        21.99 
TCGA-AP-A05D TCGA-AP-A0LF TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1C7 TCGA-AX-A1C8 
       57.80         3.39        21.90        36.13        16.96        13.55 
TCGA-AX-A2H4 TCGA-AX-A2IO TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
       30.12        64.93         0.30         0.26         0.30         0.39 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11P TCGA-B5-A11Q TCGA-B5-A1MU TCGA-B5-A1N2 
       27.29        17.85        36.82        32.09        50.89        12.79 
TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MC 
      116.25        33.11        34.13        22.06        36.49        41.52 
TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A4ZD TCGA-D1-A0ZZ 
       12.56        15.45         6.81        24.13        16.64        22.55 
TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A3DG TCGA-D1-A3JP 
       37.32        11.51        18.67         3.95         4.27        16.93 
TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       35.38         9.37        12.39        31.10        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A22X TCGA-EO-A2CG TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ 
       37.71        57.60        51.42        22.26        16.34        23.90 
TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW 
        6.90        19.27        18.84        17.62        15.09        11.08 
TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       12.59        14.40        45.76        27.35        13.84        11.38 
TCGA-EY-A54A TCGA-FI-A2CX TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 
       14.70        40.01        96.69         9.07        28.93        25.02 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W3 
        1.74         7.76         2.43        23.74         9.47        26.10 
TCGA-PG-A914 TCGA-PG-A915 
       12.92         7.00 

$`DEL PEAK 26(11Q25) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        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-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        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26         0.39        19.79         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM TCGA-AJ-A3I9 
        0.76         1.68        14.66        22.49        22.26        17.06 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        21.21        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       14.76        22.32        12.82        20.78         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        63.91 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       45.53        36.89        23.87        12.20        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        46.78        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-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-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 
       67.50        25.12        36.39        11.08         4.77        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       26.33        17.75        30.74         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
        0.20         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47        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-A11R 
       75.72        54.44        45.90        43.96        40.50        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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       11.87        15.29        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.95        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        34.98        38.37        28.27        10.72 
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 
       20.02        23.70        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-A56F 
        6.21        10.22        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-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-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-A16B 
       29.33        32.58         0.66        15.72        36.10        36.36 
TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       37.51        36.79        27.42        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-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        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-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-A2KV TCGA-DF-A2KY 
        8.48        44.88         0.26         4.11        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QY 
       27.16        16.31        39.29        36.62        24.30       110.10 
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        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.04         7.36        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        51.52        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        26.96        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GQ TCGA-EY-A1GT 
       23.34        23.34        22.78        13.97        17.88        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A215 
       12.43        15.81         6.48        19.33        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A547 TCGA-EY-A548 
       22.82        20.05        31.04        29.10        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       19.89        16.96         5.88        41.06        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F9 
        7.99        13.84         8.98        59.01        28.96        29.23 
TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC 
       41.06        45.01        14.04        13.28        18.21        23.24 
TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        23.97        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6J9 TCGA-SL-A6JA 
        0.07         0.23 

  DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE 
                        0.26                         0.07 
  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 
                      19.085                       23.900 
[1] "0.3 - 116.2 (19.1)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2"  
D77V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 26(11Q25) MUTATED                                        32
  DEL PEAK 26(11Q25) WILD-TYPE                                     363
                              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                                  54
  DEL PEAK 26(11Q25) WILD-TYPE                                58
D77V3, multiclass
                                         clus
vv                                        DEL PEAK 26(11Q25) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         32
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               54
                                         clus
vv                                        DEL PEAK 26(11Q25) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          363
  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"
D77V4, binary
                              cls
clus                             0   1
  DEL PEAK 26(11Q25) MUTATED    13  79
  DEL PEAK 26(11Q25) WILD-TYPE 128 308
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(11Q25) MUTATED     13   79
  DEL PEAK 26(11Q25) WILD-TYPE  128  308
     clus
vv    DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE
  NO                          13                          128
  YES                         79                          308
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 26(11Q25) MUTATED    60   4   5   8
  DEL PEAK 26(11Q25) WILD-TYPE 303  19  12  27
D77V5, multiclass
    clus
vv   DEL PEAK 26(11Q25) MUTATED DEL PEAK 26(11Q25) WILD-TYPE
  R0                         60                          303
  R1                          4                           19
  R2                          5                           12
  RX                          8                           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 26(11Q25) MUTATED                                  1     2
  DEL PEAK 26(11Q25) WILD-TYPE                                3    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 26(11Q25) MUTATED                          26
  DEL PEAK 26(11Q25) WILD-TYPE                        75
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 26(11Q25) MUTATED                                           1    54
  DEL PEAK 26(11Q25) WILD-TYPE                                         8   312
D77V6, multiclass
                                           clus
vv                                          DEL PEAK 26(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             54
                                           clus
vv                                          DEL PEAK 26(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           75
  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"
D77V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(11Q25) MUTATED     3  66
  DEL PEAK 26(11Q25) WILD-TYPE  11 301
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(11Q25) MUTATED      3   66
  DEL PEAK 26(11Q25) WILD-TYPE   11  301
                        clus
vv                       DEL PEAK 26(11Q25) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         66
                        clus
vv                       DEL PEAK 26(11Q25) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          301
[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    38  15
  DEL PEAK 27(12Q23.1) WILD-TYPE 419  54
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            53                            473 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                            15                             54 
$`DEL PEAK 27(12Q23.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0R6 TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 
       36.69        65.75        19.96        36.33        91.04        28.64 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LF 
       20.81        21.21        10.19        21.99        45.53         3.39 
TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A2H2 
       97.71        33.40        21.90        36.13         0.56         4.77 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A1N2 TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0YV 
       80.38        27.29        12.79        34.13        34.95        12.56 
TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S 
       15.45        10.16        24.13        22.55        39.48        18.67 
TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A2QT TCGA-DI-A2QY TCGA-EO-A1Y5 TCGA-EO-A3AZ 
        4.11        16.93        12.39       110.10        10.92        27.16 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A4KR 
       26.96        16.34        10.19        14.40        29.10        11.38 
TCGA-EY-A54A TCGA-FI-A2EU TCGA-FI-A3PV TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ 
       14.70        96.69        41.06         7.76        14.04        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A915 
       13.28        26.10        18.21        23.24         7.00 

$`DEL PEAK 27(12Q23.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        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-A2K5 TCGA-A5-A2K7 TCGA-A5-A3LO 
        9.60         8.02        46.32         5.33         5.16         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL 
       14.96         1.18        14.43        10.26         0.39        19.79 
TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       29.39         2.40        34.36        34.16         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       14.76        16.87        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        63.91        57.80        36.89        23.87        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-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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV 
       55.89        31.30        35.54        46.78        49.15         6.71 
TCGA-AP-A1E0 TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AX-A05S TCGA-AX-A05T 
       30.90        10.42        27.85        16.24        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-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-A2H4 
       54.12        67.50        25.12        36.39        11.08        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       71.24        40.80        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
       20.52         1.38         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        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-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-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-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 TCGA-BG-A0MA 
       34.98        22.06        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-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        20.02        23.70        20.12        11.31         6.81 
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-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-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-A16I 
       37.32        36.36        37.51        36.79        27.42        11.51 
TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       29.92        31.07        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26         4.27        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-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        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG 
       61.55        66.90        46.26        57.60        51.52        51.42 
TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 
       19.40        34.39        26.43        35.15        17.19        17.88 
TCGA-EO-A3KU TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC 
       22.26        14.53        24.89         6.21        14.99         4.54 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-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-A1GW 
       17.62        15.09        16.11        12.43        15.81        11.08 
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        20.05 
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        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       19.89        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       39.95         7.99        13.84         8.98        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        28.96        25.02        29.23        45.01         1.74 
TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A916 
        2.43         9.47        15.45        23.97        12.92        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44        14.07        18.28         0.07         0.23 

  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                          0.56                           0.07 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                        110.10                         191.84 
  DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE 
                         21.90                          23.47 
[1] "0.6 - 110.1 (21.9)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.9"
D78V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 27(12Q23.1) MUTATED                                        12
  DEL PEAK 27(12Q23.1) WILD-TYPE                                     383
                                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                                  38
  DEL PEAK 27(12Q23.1) WILD-TYPE                                74
D78V3, multiclass
                                         clus
vv                                        DEL PEAK 27(12Q23.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           12
  MIXED SEROUS AND ENDOMETRIOID                                      3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 38
                                         clus
vv                                        DEL PEAK 27(12Q23.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            383
  MIXED SEROUS AND ENDOMETRIOID                                       18
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V4, binary
                                cls
clus                               0   1
  DEL PEAK 27(12Q23.1) MUTATED     8  45
  DEL PEAK 27(12Q23.1) WILD-TYPE 133 342
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12Q23.1) MUTATED      8   45
  DEL PEAK 27(12Q23.1) WILD-TYPE  133  342
     clus
vv    DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE
  NO                             8                            133
  YES                           45                            342
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12Q23.1) MUTATED    33   1   4   7
  DEL PEAK 27(12Q23.1) WILD-TYPE 330  22  13  28
D78V5, multiclass
    clus
vv   DEL PEAK 27(12Q23.1) MUTATED DEL PEAK 27(12Q23.1) WILD-TYPE
  R0                           33                            330
  R1                            1                             22
  R2                            4                             13
  RX                            7                             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 27(12Q23.1) MUTATED                                  1     0
  DEL PEAK 27(12Q23.1) WILD-TYPE                                3    20
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 27(12Q23.1) MUTATED                          16
  DEL PEAK 27(12Q23.1) WILD-TYPE                        85
                                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      29
  DEL PEAK 27(12Q23.1) WILD-TYPE   337
D78V6, multiclass
                                           clus
vv                                          DEL PEAK 27(12Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                0
  BLACK OR AFRICAN AMERICAN                                           16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            0
  WHITE                                                               29
                                           clus
vv                                          DEL PEAK 27(12Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 20
  BLACK OR AFRICAN AMERICAN                                             85
  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"
D78V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12Q23.1) MUTATED     1  34
  DEL PEAK 27(12Q23.1) WILD-TYPE  13 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12Q23.1) MUTATED      1   34
  DEL PEAK 27(12Q23.1) WILD-TYPE   13  333
                        clus
vv                       DEL PEAK 27(12Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK 27(12Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 13
  NOT HISPANIC OR LATINO                            333
[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    49  14
  DEL PEAK 28(12Q24.33) WILD-TYPE 408  55
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             63                             463 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                             14                              55 
$`DEL PEAK 28(12Q24.33) MUTATED`
TCGA-5B-A90C TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LP 
       36.69        11.44        36.33        91.04        28.64        14.96 
TCGA-AJ-A23N TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH 
       14.43        29.39        18.90        20.81        21.21        10.19 
TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A3K1 TCGA-AW-A1PO 
       21.99        45.53        97.71        33.40        21.90         0.56 
TCGA-AX-A1C7 TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A3G3 
       16.96        12.43        76.83         4.77        71.24         1.38 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A0YV TCGA-BG-A18C 
       80.38        17.85        29.65        34.95        12.56        15.45 
TCGA-BK-A139 TCGA-BK-A26L TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16S TCGA-D1-A17K 
       10.16        24.13        22.55        39.48        18.67        28.08 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        2.07         4.11        12.39        31.10       110.10        48.36 
TCGA-EO-A1Y5 TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A214 
       10.92        34.39        27.16        16.34         4.54        14.40 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2EU TCGA-FI-A3PV 
       29.10        11.38        14.70         5.88        96.69        41.06 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 
        7.76        14.04        23.74        13.28        26.10        18.21 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-SL-A6J9 
       23.97         7.00         0.07 

$`DEL PEAK 28(12Q24.33) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GN TCGA-A5-A0GP TCGA-A5-A0GQ 
       57.53        65.75        60.53        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R6 
       36.82        28.27        20.81        23.21        68.65        19.96 
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-A3LO TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
        7.33         1.18        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16         1.12         0.76         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        17.06        36.99        20.65 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       15.62        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 
       36.89        23.87        12.20        20.91        48.79       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-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        46.78        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        36.13        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-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       65.88        13.28        19.20        13.55        15.25        20.28 
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        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         0.30         0.26         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        14.47         0.39        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        27.29        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-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-A3FH 
      116.25        96.30        78.81        62.14        33.11        14.27 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
        6.81        35.90        34.98         6.21        10.22        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-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-A16G 
       36.10        37.32        36.36        37.51        36.79        27.42 
TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       11.51        29.92        31.07        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       18.02        14.73         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
        1.28        28.01        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-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-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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A1LX 
       39.29        36.62        24.30        35.38         9.37        23.38 
TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       17.06         2.37         6.67        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.80        49.15        37.71        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AU 
       46.26        57.60        51.52        51.42        19.40        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KX 
       35.15        17.19        17.88        26.96        22.26        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        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        11.08         6.48        19.33        12.59 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       10.19        18.87        22.82        20.05        45.76        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        14.14        19.89        16.96 
TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       40.01        41.06        39.88        39.95         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-KP-A3W1 TCGA-PG-A5BC 
       29.23        45.01         1.74         2.43         9.47        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                           0.07                            0.13 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                         110.10                          191.84 
  DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE 
                          20.81                           23.64 
[1] "0.1 - 110.1 (20.8)" "0.1 - 191.8 (23.6)"
[1] "hr=" "2.2"
D79V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 28(12Q24.33) MUTATED                                        18
  DEL PEAK 28(12Q24.33) WILD-TYPE                                     377
                                 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                                  43
  DEL PEAK 28(12Q24.33) WILD-TYPE                                69
D79V3, multiclass
                                         clus
vv                                        DEL PEAK 28(12Q24.33) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            18
  MIXED SEROUS AND ENDOMETRIOID                                       2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  43
                                         clus
vv                                        DEL PEAK 28(12Q24.33) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             377
  MIXED SEROUS AND ENDOMETRIOID                                        19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V4, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q24.33) MUTATED     9  54
  DEL PEAK 28(12Q24.33) WILD-TYPE 132 333
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED      9   54
  DEL PEAK 28(12Q24.33) WILD-TYPE  132  333
     clus
vv    DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  NO                              9                             132
  YES                            54                             333
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(12Q24.33) MUTATED    39   2   5   8
  DEL PEAK 28(12Q24.33) WILD-TYPE 324  21  12  27
D79V5, multiclass
    clus
vv   DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
  R0                            39                             324
  R1                             2                              21
  R2                             5                              12
  RX                             8                              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 28(12Q24.33) MUTATED                                  1     1
  DEL PEAK 28(12Q24.33) WILD-TYPE                                3    19
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 28(12Q24.33) MUTATED                          16
  DEL PEAK 28(12Q24.33) WILD-TYPE                        85
                                 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      39
  DEL PEAK 28(12Q24.33) WILD-TYPE   327
D79V6, multiclass
                                           clus
vv                                          DEL PEAK 28(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                            16
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             0
  WHITE                                                                39
                                           clus
vv                                          DEL PEAK 28(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  19
  BLACK OR AFRICAN AMERICAN                                              85
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               9
  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"
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q24.33) MUTATED     1  45
  DEL PEAK 28(12Q24.33) WILD-TYPE  13 322
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q24.33) MUTATED      1   45
  DEL PEAK 28(12Q24.33) WILD-TYPE   13  322
                        clus
vv                       DEL PEAK 28(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            45
                        clus
vv                       DEL PEAK 28(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                  13
  NOT HISPANIC OR LATINO                             322
[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    71  22
  DEL PEAK 29(13Q11) WILD-TYPE 386  47
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          93                          433 
  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                          22                           47 
$`DEL PEAK 29(13Q11) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A0VP 
       41.06       149.56        65.75        60.53        17.59        42.35 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK 
       36.33        91.04        28.64         7.33        14.96         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH 
       29.39        18.90         1.64        22.26        17.06        10.19 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0L8 
       16.87        16.87        20.78        45.53        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A1C7 
      125.42        97.71        33.40        36.13        53.92        16.96 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HF 
       15.25        20.28        76.83        36.39        30.12        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3GI 
        2.96        64.93        20.52         1.38         0.30         0.39 
TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
        4.11        36.82        50.89        11.87        12.79       116.25 
TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 
       34.95        22.06        12.56        15.45         6.81        10.16 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A179 
       16.64        61.87        67.20        37.32        31.07        14.73 
TCGA-D1-A1NU TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QY 
       13.22         4.27        16.93        35.38         9.37       110.10 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GP TCGA-EY-A1GR 
       10.92        49.15        51.42        27.16        18.84        17.62 
TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX 
       15.81        11.08        20.05        45.76        29.10        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2D4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX 
       11.38        17.92         7.99        25.02        41.06        45.01 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC 
        2.43        23.74        13.28        26.10        18.21        23.24 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-SL-A6J9 
       23.97        12.92         0.07 

$`DEL PEAK 29(13Q11) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
       15.95         7.92        11.44         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
        5.33         5.16         1.18        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40        34.36        34.16         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-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        63.91        57.80        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LH 
       12.20       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        46.78        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        21.90         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-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-A1CC 
       40.11        65.88        13.28        19.20        13.55        12.43 
TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CR 
       20.05        72.56        54.12        67.50        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        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       46.49        26.33        17.75        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G6 TCGA-AX-A3G7 
        0.20         0.56        43.82         0.20         0.26         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
        1.18        18.35        14.47        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        27.29        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-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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        11.70        15.29        96.30        78.81        62.14 
TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW 
       33.11        14.27        29.65        41.06        34.13        18.61 
TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 
       20.19        19.33        20.94        35.21        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-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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC 
       20.12        11.31        35.90        34.98         6.21        10.22 
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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.11        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ 
       36.62        24.30        12.39        31.10        23.38        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        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        17.88        26.96        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        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-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS TCGA-EY-A1GT TCGA-EY-A1GU 
        6.90        19.27        17.88        15.09        16.11        12.43 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
        6.48        19.33        12.59        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       22.82        31.04        27.35        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 
       16.96         5.88        40.01        41.06        39.88        39.95 
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-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       28.96        29.23         1.74         7.76        14.04         9.47 
TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45         7.00        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE 
                        0.07                         0.13 
  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 
                       20.52                        23.70 
[1] "0.1 - 149.6 (20.5)" "0.1 - 191.8 (23.7)"
[1] "hr=" "2.1"
D80V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 29(13Q11) MUTATED                                        39
  DEL PEAK 29(13Q11) WILD-TYPE                                     356
                              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                                  50
  DEL PEAK 29(13Q11) WILD-TYPE                                62
D80V3, multiclass
                                         clus
vv                                        DEL PEAK 29(13Q11) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         39
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               50
                                         clus
vv                                        DEL PEAK 29(13Q11) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          356
  MIXED SEROUS AND ENDOMETRIOID                                     16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V4, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q11) MUTATED    17  77
  DEL PEAK 29(13Q11) WILD-TYPE 124 310
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q11) MUTATED     17   77
  DEL PEAK 29(13Q11) WILD-TYPE  124  310
     clus
vv    DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE
  NO                          17                          124
  YES                         77                          310
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 29(13Q11) MUTATED    61   5   6   8
  DEL PEAK 29(13Q11) WILD-TYPE 302  18  11  27
D80V5, multiclass
    clus
vv   DEL PEAK 29(13Q11) MUTATED DEL PEAK 29(13Q11) WILD-TYPE
  R0                         61                          302
  R1                          5                           18
  R2                          6                           11
  RX                          8                           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 29(13Q11) MUTATED                                  0     3
  DEL PEAK 29(13Q11) WILD-TYPE                                4    17
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 29(13Q11) MUTATED                          25
  DEL PEAK 29(13Q11) WILD-TYPE                        76
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 29(13Q11) MUTATED                                           2    60
  DEL PEAK 29(13Q11) WILD-TYPE                                         7   306
D80V6, multiclass
                                           clus
vv                                          DEL PEAK 29(13Q11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              3
  BLACK OR AFRICAN AMERICAN                                         25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             60
                                           clus
vv                                          DEL PEAK 29(13Q11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               17
  BLACK OR AFRICAN AMERICAN                                           76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  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"
D80V7, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q11) MUTATED     4  67
  DEL PEAK 29(13Q11) WILD-TYPE  10 300
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q11) MUTATED      4   67
  DEL PEAK 29(13Q11) WILD-TYPE   10  300
                        clus
vv                       DEL PEAK 29(13Q11) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                         67
                        clus
vv                       DEL PEAK 29(13Q11) WILD-TYPE
  HISPANIC OR LATINO                               10
  NOT HISPANIC OR LATINO                          300
[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    80  22
  DEL PEAK 30(13Q14.2) WILD-TYPE 377  47
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           102                            424 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            22                             47 
$`DEL PEAK 30(13Q14.2) MUTATED`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G2 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 
       41.06        10.29       149.56        65.75        60.53        17.59 
TCGA-A5-A0VP TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A2QK 
       42.35        36.33        91.04         7.33        14.96         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3NH 
       29.39        18.90         1.64        22.26        17.06        10.19 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A05H TCGA-AP-A05P TCGA-AP-A0LI 
       16.87        16.87        20.78        45.53        20.91        97.71 
TCGA-AP-A0LO TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C9 TCGA-AX-A1CF 
       33.40        36.13         0.56        53.92        15.25        76.83 
TCGA-AX-A1CK TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FW TCGA-AX-A3FX 
       67.50        36.39        30.12         2.96         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0K3 
       20.52         1.38         0.30         0.26         0.39        27.29 
TCGA-B5-A0KB TCGA-B5-A11P TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 
        4.11        36.82        50.89        11.87        12.79       116.25 
TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A2AE 
       33.11        34.95        22.06        12.56        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
        6.81        10.22        10.16        16.64        61.87        67.20 
TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU 
       37.32        31.07         3.95        14.73        28.08        13.22 
TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-E6-A8L9 TCGA-EO-A1Y7 
        4.27        16.93        35.38         9.37        27.32        49.15 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GV 
       34.39        27.16         4.54        18.84        17.62        15.81 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3QX 
       11.08        12.59        20.05        45.76        29.10        13.84 
TCGA-EY-A547 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV 
       17.92         9.07        28.93        25.02        29.23        41.06 
TCGA-FI-A3PX TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       45.01         7.76        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-SL-A6J9 
        9.47        26.10        18.21        23.24        23.97         0.07 

$`DEL PEAK 30(13Q14.2) WILD-TYPE`
TCGA-5B-A90C TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB 
       36.69       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 
      112.54       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-A2K4 
        7.92        11.44         9.60         8.02        46.32        28.64 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
        5.33         5.16         1.18        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
        2.40        34.36        34.16         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NF 
       14.66        22.49        20.81        36.99        20.65        21.21 
TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.62        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-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        63.91        57.80        36.89        23.87 
TCGA-AP-A05O TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       12.20        48.79       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-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        46.78        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        21.90 
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-A1C8 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ 
       13.55        20.28        12.43        20.05        72.56        54.12 
TCGA-AX-A1CN TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        11.08         4.77        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ 
       30.74        31.13        64.93         0.23         0.20         0.20 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR 
        0.30         1.18        18.35        14.47        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-A0K4 TCGA-B5-A0K6 
       28.64        28.34        30.51        25.91        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-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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC 
       14.70        11.70        15.29        96.30        78.81        62.14 
TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       14.27        29.65        41.06        34.13        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M8 
       19.33        20.94        35.21        34.98        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-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98         6.21        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        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-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-A16S TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
       10.65         0.69        18.67         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
        6.64        30.15        18.02         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NW TCGA-D1-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        36.62        24.30        12.39        31.10       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S 
        7.36        16.80        10.92        37.71        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CG TCGA-EO-A2CH 
       66.90        46.26        57.60        51.52        51.42        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU 
       26.43        35.15        17.19        17.88        26.96        22.26 
TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       16.34        14.53        24.89         6.21        14.99        53.88 
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-A1GS TCGA-EY-A1GT 
       13.97         6.90        19.27        17.88        15.09        16.11 
TCGA-EY-A1GU TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A215 
       12.43         6.48        19.33        10.19        14.40        18.87 
TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 
       22.82        31.04        27.35        11.38        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW 
       39.95         7.99        13.84         8.98        96.69        59.01 
TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A915 TCGA-PG-A916 
       28.96         1.74        15.45        12.92         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
        4.44        14.07        18.28         0.23 

  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                          0.07                           0.13 
  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 
                        20.285                         23.885 
[1] "0.1 - 149.6 (20.3)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.3"
D81V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                        51
  DEL PEAK 30(13Q14.2) WILD-TYPE                                     344
                                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                                  46
  DEL PEAK 30(13Q14.2) WILD-TYPE                                66
D81V3, multiclass
                                         clus
vv                                        DEL PEAK 30(13Q14.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           51
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 46
                                         clus
vv                                        DEL PEAK 30(13Q14.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            344
  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"
D81V4, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED    17  86
  DEL PEAK 30(13Q14.2) WILD-TYPE 124 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     17   86
  DEL PEAK 30(13Q14.2) WILD-TYPE  124  301
     clus
vv    DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  NO                            17                            124
  YES                           86                            301
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(13Q14.2) MUTATED    67   2   5   7
  DEL PEAK 30(13Q14.2) WILD-TYPE 296  21  12  28
D81V5, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  R0                           67                            296
  R1                            2                             21
  R2                            5                             12
  RX                            7                             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 30(13Q14.2) MUTATED                                  0     2
  DEL PEAK 30(13Q14.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 30(13Q14.2) MUTATED                          28
  DEL PEAK 30(13Q14.2) WILD-TYPE                        73
                                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      66
  DEL PEAK 30(13Q14.2) WILD-TYPE   300
D81V6, multiclass
                                           clus
vv                                          DEL PEAK 30(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               66
                                           clus
vv                                          DEL PEAK 30(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  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"
D81V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED     5  77
  DEL PEAK 30(13Q14.2) WILD-TYPE   9 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED      5   77
  DEL PEAK 30(13Q14.2) WILD-TYPE    9  290
                        clus
vv                       DEL PEAK 30(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       DEL PEAK 30(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            290
[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    57  14
  DEL PEAK 31(14Q13.1) WILD-TYPE 400  55
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            71                            455 
  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                            14                             55 
$`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        29.39 
TCGA-AJ-A3BD TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EL TCGA-AJ-A3NH TCGA-AJ-A6NU 
       34.16        18.90         1.64        22.49        10.19        20.78 
TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LO TCGA-AP-A1E0 TCGA-AX-A0IW 
       45.53        48.79       125.42        33.40        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         0.56        20.52 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.26         0.30         0.39        80.38        17.85         4.11 
TCGA-B5-A11P TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A18C 
       36.82        11.87        12.79        29.65        34.13        15.45 
TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-D1-A16I TCGA-D1-A179 TCGA-D1-A1NU 
       10.22        10.16        16.64        11.51        14.73        13.22 
TCGA-D1-A1NW TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A2QT TCGA-E6-A8L9 TCGA-EO-A2CG 
        0.72        16.93        35.38        12.39        27.32        51.42 
TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GJ TCGA-EY-A1GO TCGA-EY-A1GR 
       34.39        22.26        16.34        23.90        19.27        17.62 
TCGA-EY-A1GS TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A 
       15.09        14.40        45.76        29.10        11.38        14.70 
TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR 
       41.06        96.69        25.02        29.23        45.01         1.74 
TCGA-JU-AAVI TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        7.76        23.97         7.00         4.44         0.07 

$`DEL PEAK 31(14Q13.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ 
       74.10        57.53        65.75        60.53        46.55        38.37 
TCGA-A5-A0GR TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 
       36.82        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-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        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK 
       19.79         2.40        34.36         1.12         0.76         1.68 
TCGA-AJ-A3EK TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE 
       14.66        22.26        17.06        20.81        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       16.87        22.32        12.82         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        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD 
       57.80        36.89        23.87        12.20        20.91       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-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-A1E1 TCGA-AP-A1E3 
       35.54        46.78        49.15         6.71        10.42        27.85 
TCGA-AP-A1E4 TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T 
       16.24        21.90        36.13         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-A1C8 TCGA-AX-A1C9 
       65.88        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-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2H8 
       25.12        36.39        30.12        71.24        40.80        61.18 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH 
       81.37        34.32        46.49        19.36        26.33        17.75 
TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FX 
       30.74        31.13        64.93         0.23         0.20        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         1.38         0.30         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        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        27.29 
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-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-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-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        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        22.06        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-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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C 
        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-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         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D 
       30.15        18.02         1.58         7.00         0.99        30.44 
TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
        1.28        28.01        28.08        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-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-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        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       110.10 
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        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A22R 
        7.36        16.80        10.92        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH 
       61.55        66.90        46.26        57.60        51.52        19.40 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 
       26.43        35.15        17.19        27.16        17.88        26.96 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
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-A1GQ TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV 
        6.90        18.84        17.88        16.11        12.43        15.81 
TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
       11.08         6.48        19.33        12.59        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 
       22.82        20.05        31.04        27.35        13.84        17.92 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
       14.14        19.89        16.96         5.88        40.01        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       39.95         7.99        13.84         8.98        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       28.93        28.96        41.06        14.04         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       13.28         9.47        26.10        18.21        23.24        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.23 

  DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE 
                          0.07                           0.13 
  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 
                         17.85                          23.93 
[1] "0.1 - 125.4 (17.9)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.2"
D82V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 31(14Q13.1) MUTATED                                        25
  DEL PEAK 31(14Q13.1) WILD-TYPE                                     370
                                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                                  41
  DEL PEAK 31(14Q13.1) WILD-TYPE                                71
D82V3, multiclass
                                         clus
vv                                        DEL PEAK 31(14Q13.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           25
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 41
                                         clus
vv                                        DEL PEAK 31(14Q13.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            370
  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"
D82V4, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q13.1) MUTATED    16  55
  DEL PEAK 31(14Q13.1) WILD-TYPE 125 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q13.1) MUTATED     16   55
  DEL PEAK 31(14Q13.1) WILD-TYPE  125  332
     clus
vv    DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE
  NO                            16                            125
  YES                           55                            332
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(14Q13.1) MUTATED    45   3   2   4
  DEL PEAK 31(14Q13.1) WILD-TYPE 318  20  15  31
D82V5, multiclass
    clus
vv   DEL PEAK 31(14Q13.1) MUTATED DEL PEAK 31(14Q13.1) WILD-TYPE
  R0                           45                            318
  R1                            3                             20
  R2                            2                             15
  RX                            4                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(14Q13.1) MUTATED                                  1     1
  DEL PEAK 31(14Q13.1) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 31(14Q13.1) MUTATED                          25
  DEL PEAK 31(14Q13.1) WILD-TYPE                        76
                                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      38
  DEL PEAK 31(14Q13.1) WILD-TYPE   328
D82V6, multiclass
                                           clus
vv                                          DEL PEAK 31(14Q13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               38
                                           clus
vv                                          DEL PEAK 31(14Q13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  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"
D82V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q13.1) MUTATED     3  47
  DEL PEAK 31(14Q13.1) WILD-TYPE  11 320
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q13.1) MUTATED      3   47
  DEL PEAK 31(14Q13.1) WILD-TYPE   11  320
                        clus
vv                       DEL PEAK 31(14Q13.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           47
                        clus
vv                       DEL PEAK 31(14Q13.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            320
[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   105  30
  DEL PEAK 32(15Q15.1) WILD-TYPE 352  39
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           135                            391 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                            30                             39 
$`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 
       29.39        34.16        18.90         1.64        22.26        20.81 
TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 
       21.21        10.19        16.87        20.78        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        46.78        21.90        36.13         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 
       64.93         0.23         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB 
        0.26         0.39        80.38        27.29        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-A3S1 TCGA-B5-A5OE TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C 
      116.25        29.65        34.95        36.49        12.56        15.45 
TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 
       10.16        24.13        16.64        61.87        67.20        49.55 
TCGA-D1-A0ZP TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       29.95         8.55        22.55        37.32        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1O0 
       18.67         3.95        14.73        13.22         0.72         2.07 
TCGA-D1-A3DG TCGA-D1-A3DH TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY 
        4.27         4.11        35.38         9.37        31.10       110.10 
TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH 
       48.36        27.32        10.92        37.71        51.42        19.40 
TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       34.39        27.16        26.96        22.26        16.34         4.54 
TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
       19.27        18.84        15.09        11.08        12.59        10.19 
TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR 
       14.40        20.05        45.76        29.10        27.35        11.38 
TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 
       17.92        39.95        96.69        59.01        28.93        25.02 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 
       29.23        41.06        45.01        14.04        23.74        13.28 
TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       26.10        18.21        23.24        23.97        12.92         7.00 
TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SL-A6J9 
        4.44        14.07         0.07 

$`DEL PEAK 32(15Q15.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        23.21        68.65        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-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
        5.33         5.16         1.18        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK 
        2.40        34.36         1.12         0.76         1.68        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ 
       22.49        17.06        36.99        20.65        15.62        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT 
       15.95        14.76        16.87        22.32        12.82         2.70 
TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A 
        0.13        83.67        23.31        86.07         8.22        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        36.89        23.87        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-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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       10.42        27.85        16.24        13.58        19.82        29.69 
TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 
       68.35        72.03        46.45        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-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       16.96        13.55        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA 
       25.12        36.39         4.77        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       34.32        46.49        26.33        17.75        30.74        31.13 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.56        43.82         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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-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-A3FD 
       11.70        15.29        96.30        78.81        62.14        33.11 
TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       14.27        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        22.06        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        20.02        23.70        20.12        11.31 
TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A13B 
        6.81        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-A0ZR TCGA-D1-A0ZS TCGA-D1-A0ZU 
       66.48        16.83        19.79         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-A16X TCGA-D1-A16Y 
       29.92        33.63        10.65         0.69         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-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-A1O5 
       22.92         1.41        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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        0.26        16.93        89.33        10.92        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-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 
        2.37         6.67        16.04         7.36        16.80        49.15 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 
       26.43        35.15        17.19        17.88        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        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-A1GX TCGA-EY-A1H0 
       17.62        16.11        12.43        15.81         6.48        19.33 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 
       18.87        22.82        31.04        13.84        14.14        19.89 
TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 
       14.70        16.96         5.88        40.01        41.06        39.88 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-H5-A2HR 
        7.99        13.84         8.98         9.07        28.96         1.74 
TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
        7.76         2.43         9.47        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZJ 
       18.84        39.95        12.92        23.64        14.83        18.28 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                          0.07                           0.13 
  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 
                         20.81                          23.90 
[1] "0.1 - 116.2 (20.8)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.5"
D83V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                        52
  DEL PEAK 32(15Q15.1) WILD-TYPE                                     343
                                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                                  75
  DEL PEAK 32(15Q15.1) WILD-TYPE                                37
D83V3, multiclass
                                         clus
vv                                        DEL PEAK 32(15Q15.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           52
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 75
                                         clus
vv                                        DEL PEAK 32(15Q15.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            343
  MIXED SEROUS AND ENDOMETRIOID                                       12
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V4, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.1) MUTATED    25 111
  DEL PEAK 32(15Q15.1) WILD-TYPE 116 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED     25  111
  DEL PEAK 32(15Q15.1) WILD-TYPE  116  276
     clus
vv    DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  NO                            25                            116
  YES                          111                            276
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q15.1) MUTATED    83   7   8  13
  DEL PEAK 32(15Q15.1) WILD-TYPE 280  16   9  22
D83V5, multiclass
    clus
vv   DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  R0                           83                            280
  R1                            7                             16
  R2                            8                              9
  RX                           13                             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 32(15Q15.1) MUTATED                                  1     2
  DEL PEAK 32(15Q15.1) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 32(15Q15.1) MUTATED                          35
  DEL PEAK 32(15Q15.1) WILD-TYPE                        66
                                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      84
  DEL PEAK 32(15Q15.1) WILD-TYPE   282
D83V6, multiclass
                                           clus
vv                                          DEL PEAK 32(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           35
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               84
                                           clus
vv                                          DEL PEAK 32(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             66
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  WHITE                                                                282
[1] 5 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  98
  DEL PEAK 32(15Q15.1) WILD-TYPE  11 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED      3   98
  DEL PEAK 32(15Q15.1) WILD-TYPE   11  269
                        clus
vv                       DEL PEAK 32(15Q15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           98
                        clus
vv                       DEL PEAK 32(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            269
[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    92  21
  DEL PEAK 33(15Q23) WILD-TYPE 365  48
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                         113                          413 
  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                          21                           48 
$`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        14.43         0.39 
TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3EM 
       29.39        34.16         1.12        18.90         1.64        22.26 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       20.81        21.21        10.19        16.87        16.87        20.78 
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        21.90        36.13 
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        64.93 
TCGA-AX-A3FS TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI 
        0.23         0.20         1.38         0.26         0.30         0.39 
TCGA-B5-A0JN TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
       80.38        17.85         4.11        75.72        36.82       102.31 
TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3S1 TCGA-BG-A0M8 TCGA-BG-A0MT 
       11.87        12.79       116.25        29.65        36.49        21.17 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
       15.45         6.81        24.13        16.64        61.87        67.20 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A16V 
        8.55        22.55        11.51        31.07        18.67         3.95 
TCGA-D1-A1NU TCGA-D1-A3DH TCGA-DI-A1NO TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 
       13.22         4.11         9.37        48.36        27.32        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU 
       37.71        51.42        19.40        27.16        26.96        22.26 
TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A212 
       16.34         4.54        19.27        18.84        15.09        10.19 
TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A 
       14.40        45.76        27.35        11.38        17.92        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR 
       39.95        96.69        59.01        28.93        25.02         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A5BC 
        7.76        14.04        23.74        13.28        26.10        23.24 
TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SJ-A6ZI 
       23.97        12.92         7.00         4.44        14.07 

$`DEL PEAK 33(15Q23) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        23.21        68.65        19.59        24.62 
TCGA-A5-A0RA TCGA-A5-A0VP TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OH TCGA-A5-A1OJ 
       29.06        42.35        15.95         7.92        36.33         9.60 
TCGA-A5-A1OK TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23M TCGA-AJ-A23O TCGA-AJ-A2QL 
        8.02         5.33         5.16         1.18        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
        2.40        34.36         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 
       17.06        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       14.76        22.32        12.82         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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        12.20        20.91       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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 TCGA-AP-A1E1 
       35.54        46.78        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-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-A1CE TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ 
       16.96        13.55        20.05        76.83        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        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G4 
       31.13         0.20         0.56        43.82        20.52         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        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        27.29        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-A1MU TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ 
      191.84        50.89        14.40        14.70        11.70        15.29 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FD TCGA-B5-A3FH TCGA-B5-A5OC 
       96.30        78.81        62.14        33.11        14.27        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        22.06        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-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-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        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C 
       34.98         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-A0TE TCGA-BS-A0TG TCGA-BS-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        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-A0ZR TCGA-D1-A0ZS 
       66.48        16.83        19.79        29.95         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-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-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW 
       11.15        24.30         2.33        22.92         1.41         0.72 
TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 
       18.25        16.87        18.02         2.07        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QU 
       39.29        36.62        24.30        35.38        12.39        31.10 
TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
      110.10        23.38        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.52        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       17.19        17.88        14.53        24.89         6.21        14.99 
TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ 
       53.88        24.36        27.16        23.34        23.34        23.90 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GQ TCGA-EY-A1GR TCGA-EY-A1GT 
       22.78        13.97         6.90        17.88        17.62        16.11 
TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A210 
       12.43        15.81        11.08         6.48        19.33        12.59 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3QX 
       18.87        22.82        20.05        31.04        29.10        13.84 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       14.14        19.89        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EX TCGA-FI-A2F4 
       39.88         7.99        13.84         8.98         9.07        28.96 
TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W4 
       29.23        41.06        45.01         2.43         9.47        18.21 
TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ 
       15.45        11.24         6.97        18.84        39.95        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        18.28         0.07         0.23 

  DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE 
                        0.20                         0.07 
  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 
                       19.36                        24.62 
[1] "0.2 - 125.4 (19.4)" "0.1 - 191.8 (24.6)"
[1] "hr=" "1.9"
D84V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 33(15Q23) MUTATED                                        38
  DEL PEAK 33(15Q23) WILD-TYPE                                     357
                              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                                  68
  DEL PEAK 33(15Q23) WILD-TYPE                                44
D84V3, multiclass
                                         clus
vv                                        DEL PEAK 33(15Q23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         38
  MIXED SEROUS AND ENDOMETRIOID                                    7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               68
                                         clus
vv                                        DEL PEAK 33(15Q23) 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"
D84V4, binary
                              cls
clus                             0   1
  DEL PEAK 33(15Q23) MUTATED    22  91
  DEL PEAK 33(15Q23) WILD-TYPE 119 296
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(15Q23) MUTATED     22   91
  DEL PEAK 33(15Q23) WILD-TYPE  119  296
     clus
vv    DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE
  NO                          22                          119
  YES                         91                          296
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 33(15Q23) MUTATED    75   4   6   9
  DEL PEAK 33(15Q23) WILD-TYPE 288  19  11  26
D84V5, multiclass
    clus
vv   DEL PEAK 33(15Q23) MUTATED DEL PEAK 33(15Q23) WILD-TYPE
  R0                         75                          288
  R1                          4                           19
  R2                          6                           11
  RX                          9                           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 33(15Q23) MUTATED                                  0     2
  DEL PEAK 33(15Q23) WILD-TYPE                                4    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 33(15Q23) MUTATED                          32
  DEL PEAK 33(15Q23) WILD-TYPE                        69
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 33(15Q23) MUTATED                                           1    68
  DEL PEAK 33(15Q23) WILD-TYPE                                         8   298
D84V6, multiclass
                                           clus
vv                                          DEL PEAK 33(15Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   0
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         32
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             68
                                           clus
vv                                          DEL PEAK 33(15Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     4
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           69
  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"
D84V7, binary
                              cls
clus                             0   1
  DEL PEAK 33(15Q23) MUTATED     1  81
  DEL PEAK 33(15Q23) WILD-TYPE  13 286
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(15Q23) MUTATED      1   81
  DEL PEAK 33(15Q23) WILD-TYPE   13  286
                        clus
vv                       DEL PEAK 33(15Q23) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         81
                        clus
vv                       DEL PEAK 33(15Q23) WILD-TYPE
  HISPANIC OR LATINO                               13
  NOT HISPANIC OR LATINO                          286
[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    70  19
  DEL PEAK 34(16P13.3) WILD-TYPE 387  50
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            89                            437 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            19                             50 
$`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        29.39         1.12        20.81        10.19        16.87 
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        46.78 
TCGA-AP-A3K1 TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CC 
       21.90         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        64.93 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K8 
        1.38         0.26         0.39        43.13        27.29        17.85 
TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A3FD 
        4.11        75.72        36.82       102.31        11.87        33.11 
TCGA-B5-A3S1 TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 
       29.65        34.95        15.45         6.81        10.22        10.16 
TCGA-BK-A4ZD TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S 
       16.64        49.55        22.55        11.51        31.07        18.67 
TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN 
       13.22         0.72         4.27         4.11        16.93        35.38 
TCGA-DI-A1NO TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
        9.37       110.10        27.32        10.92        49.15        37.71 
TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EY-A1GR TCGA-EY-A210 TCGA-EY-A212 
       51.42        27.16        26.96        17.62        12.59        10.19 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV 
       29.10        27.35        13.84        96.69        28.93        41.06 
TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W4 
       45.01         1.74         7.76         2.43        23.74        18.21 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.24        23.97         7.00         4.44         0.07 

$`DEL PEAK 34(16P13.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        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-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K5 TCGA-A5-A2K7 
        9.60         8.02        91.04        46.32         5.33         5.16 
TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN 
       14.96        14.43        10.26         0.39        19.79         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
       34.36        34.16         0.76        18.90         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        17.06        36.99        20.65 
TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       21.21        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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        63.91        57.80 
TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE 
       36.89        23.87        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-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        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-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-A1CA TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       16.96        20.28        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        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       46.49        19.36        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       31.13         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       20.52         0.30         0.30         1.18        18.35        14.47 
TCGA-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-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-A11Q 
       88.34        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-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-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX 
       62.14        14.27        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        22.06        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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-A16G TCGA-D1-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V 
       27.42        29.92        33.63        10.65         0.69         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NX 
       11.15        24.30         2.33        22.92         1.41        18.25 
TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 
       16.87        18.02         2.07        15.06         1.05         3.95 
TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA TCGA-DF-A2KV 
        3.52        41.42         8.48        44.88         0.26        89.33 
TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 
       10.92        27.16        16.31        39.29        36.62        24.30 
TCGA-DI-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        16.04         7.36        16.80        61.74        61.55 
TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS 
       66.90        46.26        57.60        51.52        19.40        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW 
       26.43        35.15        17.19        17.88        22.26        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
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        11.08         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        20.05        45.76        31.04 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       11.38        17.92        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
        5.88        40.01        41.06        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F8 
       13.84         8.98        59.01         9.07        28.96        25.02 
TCGA-FI-A2F9 TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 TCGA-PG-A6IB 
       29.23        14.04        13.28         9.47        26.10        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.23 

  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                          0.07                           0.13 
  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 
                         21.90                          23.47 
[1] "0.1 - 125.4 (21.9)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.1"
D85V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 34(16P13.3) MUTATED                                        26
  DEL PEAK 34(16P13.3) WILD-TYPE                                     369
                                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                                  59
  DEL PEAK 34(16P13.3) WILD-TYPE                                53
D85V3, multiclass
                                         clus
vv                                        DEL PEAK 34(16P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           26
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 59
                                         clus
vv                                        DEL PEAK 34(16P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            369
  MIXED SEROUS AND ENDOMETRIOID                                       16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D85V4, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    17  73
  DEL PEAK 34(16P13.3) WILD-TYPE 124 314
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     17   73
  DEL PEAK 34(16P13.3) WILD-TYPE  124  314
     clus
vv    DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  NO                            17                            124
  YES                           73                            314
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16P13.3) MUTATED    53   6   5   8
  DEL PEAK 34(16P13.3) WILD-TYPE 310  17  12  27
D85V5, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  R0                           53                            310
  R1                            6                             17
  R2                            5                             12
  RX                            8                             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 34(16P13.3) MUTATED                                  0     2
  DEL PEAK 34(16P13.3) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 34(16P13.3) MUTATED                          28
  DEL PEAK 34(16P13.3) WILD-TYPE                        73
                                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      53
  DEL PEAK 34(16P13.3) WILD-TYPE   313
D85V6, multiclass
                                           clus
vv                                          DEL PEAK 34(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               53
                                           clus
vv                                          DEL PEAK 34(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             73
  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"
D85V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED     2  61
  DEL PEAK 34(16P13.3) WILD-TYPE  12 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED      2   61
  DEL PEAK 34(16P13.3) WILD-TYPE   12  306
                        clus
vv                       DEL PEAK 34(16P13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           61
                        clus
vv                       DEL PEAK 34(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            306
[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   122  27
  DEL PEAK 35(16Q21) WILD-TYPE 335  42
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                         149                          377 
  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                          27                           42 
$`DEL PEAK 35(16Q21) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG 
       36.69        87.32        65.75        60.53        17.59        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M 
       36.33        91.04        28.64         7.33        14.96         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EM TCGA-AJ-A3NF 
       14.43         0.39        29.39        34.16        22.26        21.21 
TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D 
       10.19        16.87        20.78        21.99         5.95        57.80 
TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ 
       45.53        36.89        48.79         3.39        97.71        46.78 
TCGA-AW-A1PO TCGA-AX-A05U TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 
        0.56        29.69        53.92        28.54        37.78        16.96 
TCGA-AX-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP 
       15.25        20.28        12.43        72.56        25.12        36.39 
TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HD TCGA-AX-A2HF 
       11.08        30.12        71.24        61.18        46.49        19.36 
TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
        2.96        64.93         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT 
        1.38         0.30         0.26         0.30         0.39        43.13 
TCGA-B5-A0K6 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11G TCGA-B5-A11I TCGA-B5-A11P 
       13.74        17.85         4.11       113.36        75.72        36.82 
TCGA-B5-A1MS TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OE 
      102.31        11.87        12.79        33.11        29.65        34.95 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MU TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0YV 
       22.06        36.49        20.28        24.39        16.34        12.56 
TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 
       13.78        15.45        23.70        16.64        61.87        49.55 
TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N 
       22.55        39.48        27.42        11.51        29.92        31.07 
TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17R TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
       14.73        28.08        11.15        13.22         0.72        18.25 
TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO 
        2.07         4.27         4.11        16.93        35.38         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y7 
       31.10       110.10        48.36        27.32        10.92        49.15 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AZ TCGA-EO-A3B1 
       37.71        51.42        19.40        34.39        27.16        26.96 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR 
       22.26        16.34         4.54        23.90         6.90        17.62 
TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OQ 
       15.09        15.81        12.59        10.19        14.40        29.10 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CY 
       27.35        13.84        11.38        17.92        14.70        41.06 
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-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-KP-A3W4 
       45.01         1.74         2.43        23.74        26.10        18.21 
TCGA-PG-A7D5 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.97         7.00         4.44         0.07         0.23 

$`DEL PEAK 35(16Q21) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54       105.37        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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
       42.35        15.95         7.92         9.60         8.02        46.32 
TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO 
        5.33         5.16        10.26        19.79         2.40        34.36 
TCGA-AJ-A3BF TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK 
        1.12         0.76        18.90         1.68         1.64        14.66 
TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG 
       22.49        17.06        20.81        36.99        20.65        15.62 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 
        2.70         0.13        83.67        23.31        86.07         8.22 
TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD 
       63.91        23.87        12.20        20.91       125.42       117.99 
TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH TCGA-AP-A0LJ TCGA-AP-A0LL TCGA-AP-A0LM 
      110.37        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-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Y 
       21.90        36.13        13.58        19.82        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-A0IZ 
       51.09        27.39        30.02        60.66        35.01        43.82 
TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C8 TCGA-AX-A1CE 
       40.11        65.88        13.28        19.20        13.55        20.05 
TCGA-AX-A1CF TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA 
       76.83        54.12        67.50         4.77        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS 
       34.32        26.33        17.75        30.74        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR 
        0.20         1.18        18.35        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-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K7 
       28.34        30.51        25.91        27.29        17.88        17.10 
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-A3FH TCGA-B5-A5OC TCGA-B5-A5OD 
       96.30        78.81        62.14        14.27        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 
       20.02        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0U9 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL 
       97.41        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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       36.79        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       26.37        10.22         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       22.92         1.41        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        12.39        23.38        17.06         2.37         6.67 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
       16.04         7.36        16.80        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        51.52        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       17.88        14.53        24.89         6.21        14.99        53.88 
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-A1GW 
       19.27        18.84        17.88        16.11        12.43        11.08 
TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO 
        6.48        19.33        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX 
       31.04        14.14        19.89        16.96         5.88        40.01 
TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 
       39.88        39.95         7.99        13.84         8.98        28.96 
TCGA-FI-A2F9 TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-PG-A5BC 
       29.23         7.76        14.04        13.28         9.47        23.24 
TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       15.45        12.92        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83        14.07        18.28 

  DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE 
                        0.07                         0.13 
  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 
                       21.99                        23.64 
[1] "0.1 - 113.4 (22.0)" "0.1 - 191.8 (23.6)"
[1] "hr=" "1.9"
D86V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 35(16Q21) MUTATED                                        63
  DEL PEAK 35(16Q21) WILD-TYPE                                     332
                              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                                  79
  DEL PEAK 35(16Q21) WILD-TYPE                                33
D86V3, multiclass
                                         clus
vv                                        DEL PEAK 35(16Q21) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         63
  MIXED SEROUS AND ENDOMETRIOID                                    8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               79
                                         clus
vv                                        DEL PEAK 35(16Q21) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          332
  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"
D86V4, binary
                              cls
clus                             0   1
  DEL PEAK 35(16Q21) MUTATED    32 118
  DEL PEAK 35(16Q21) WILD-TYPE 109 269
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(16Q21) MUTATED     32  118
  DEL PEAK 35(16Q21) WILD-TYPE  109  269
     clus
vv    DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE
  NO                          32                          109
  YES                        118                          269
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 35(16Q21) MUTATED    95   8   8  10
  DEL PEAK 35(16Q21) WILD-TYPE 268  15   9  25
D86V5, multiclass
    clus
vv   DEL PEAK 35(16Q21) MUTATED DEL PEAK 35(16Q21) WILD-TYPE
  R0                         95                          268
  R1                          8                           15
  R2                          8                            9
  RX                         10                           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 35(16Q21) MUTATED                                  1     2
  DEL PEAK 35(16Q21) WILD-TYPE                                3    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 35(16Q21) MUTATED                          40
  DEL PEAK 35(16Q21) WILD-TYPE                        61
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 35(16Q21) MUTATED                                           2    95
  DEL PEAK 35(16Q21) WILD-TYPE                                         7   271
D86V6, multiclass
                                           clus
vv                                          DEL PEAK 35(16Q21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         40
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          2
  WHITE                                                             95
                                           clus
vv                                          DEL PEAK 35(16Q21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            7
  WHITE                                                              271
[1] 5 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     3 108
  DEL PEAK 35(16Q21) WILD-TYPE  11 259
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(16Q21) MUTATED      3  108
  DEL PEAK 35(16Q21) WILD-TYPE   11  259
                        clus
vv                       DEL PEAK 35(16Q21) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        108
                        clus
vv                       DEL PEAK 35(16Q21) WILD-TYPE
  HISPANIC OR LATINO                               11
  NOT HISPANIC OR LATINO                          259
[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   127  26
  DEL PEAK 36(16Q22.3) WILD-TYPE 330  43
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                           153                            373 
  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                            26                             43 
$`DEL PEAK 36(16Q22.3) MUTATED`
TCGA-5B-A90C TCGA-A5-A0G5 TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR 
       36.69        37.02        87.32        65.75        60.53        36.82 
TCGA-A5-A0R6 TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO 
       19.96        17.59        11.44        91.04        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM TCGA-AJ-A3BD 
       14.96         1.18        14.43         0.39        29.39        34.16 
TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW 
        1.12        18.90        22.26        21.21        10.19        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A0L8 
       20.78        21.99        63.91        57.80        36.89        48.79 
TCGA-AP-A0LF TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A05U TCGA-AX-A05Y 
        3.39        97.71        46.78         0.56        29.69        72.03 
TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       53.92        28.54        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A1CR 
       12.43        76.83        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        46.49        19.36         2.96 
TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 
       64.93         0.56        43.82         0.20        20.52         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K6 
        0.30         0.26         0.30         0.39        43.13        13.74 
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-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MU 
       12.79        33.11        34.95        22.06        36.49        20.28 
TCGA-BG-A0VT TCGA-BG-A0VW TCGA-BG-A0YV TCGA-BG-A186 TCGA-BG-A18C TCGA-BG-A2AE 
       24.39        16.34        12.56        13.78        15.45        23.70 
TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0V8 TCGA-D1-A0ZZ 
       10.22        24.13        16.64        61.87        49.55        22.55 
TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A179 
       27.42        11.51        29.92        31.07        18.67        14.73 
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-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO 
        2.07         4.27         4.11        16.93        35.38         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG 
       31.10       110.10        48.36        10.92        37.71        51.42 
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-A1GC TCGA-EY-A1GK TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GV TCGA-EY-A210 
        4.54        22.78         6.90        17.62        15.81        12.59 
TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A54A 
       14.40        29.10        27.35        13.84        17.92        14.70 
TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2EY 
        5.88        41.06        96.69        59.01         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       25.02        29.23        41.06        45.01         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       13.28        26.10        18.21        23.97        12.92         7.00 
TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
        4.44         0.07         0.23 

$`DEL PEAK 36(16Q22.3) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       41.06        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM 
       32.78       112.54       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-A3BK 
       10.26        19.79         2.40        34.36         0.76         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        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS 
       20.65        15.62        15.35        15.95        14.76        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 
       22.32        12.82         2.70         0.13        83.67         5.95 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05H TCGA-AP-A05N TCGA-AP-A05O 
       23.31        86.07         8.22        45.53        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LH 
       20.91       125.42       117.99       110.37        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-A3K1 TCGA-AP-A5FX TCGA-AX-A05S 
       10.42        27.85        16.24        21.90        36.13        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-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-A0IW TCGA-AX-A0IZ TCGA-AX-A0J0 TCGA-AX-A0J1 TCGA-AX-A1C4 
       35.01        37.78        43.82        40.11        65.88        13.28 
TCGA-AX-A1C5 TCGA-AX-A1CE TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A2H2 TCGA-AX-A2H7 
       19.20        20.05        54.12        67.50         4.77        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       81.37        34.32        26.33        17.75        30.74        31.13 
TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN 
        0.23         0.20         1.18        18.35        14.47        80.38 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX TCGA-B5-A0JY 
       56.91        46.75        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        27.29        17.88 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H 
       17.10        17.85        11.01         8.71       185.79        88.34 
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-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-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       15.29       116.25        96.30        78.81        62.14        14.27 
TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 
       29.65        41.06        34.13        18.61        20.19        19.33 
TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA 
       20.94        35.21        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        20.02        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-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-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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R 
       36.36        37.51        36.79        33.63        10.65         0.69 
TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 
        3.95         3.65        17.49        19.53         6.64        30.15 
TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       18.02         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17S TCGA-D1-A17T 
       28.01        26.37         1.51         1.78        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       22.92         1.41        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A2G7 TCGA-D1-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       24.30        12.39        23.38        17.06         2.37         6.67 
TCGA-E6-A8L9 TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R 
       27.32        16.04         7.36        16.80        49.15        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU 
       61.55        66.90        46.26        57.60        51.52        26.43 
TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       35.15        17.19        17.88        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ TCGA-EY-A1GS 
       23.90        13.97        19.27        18.84        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GW TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A212 
       16.11        12.43        11.08         6.48        19.33        10.19 
TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR 
       18.87        22.82        20.05        45.76        31.04        11.38 
TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 
       14.14        19.89        16.96        40.01        39.88        39.95 
TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-H5-A2HR TCGA-JU-AAVI 
        7.99        13.84         8.98        28.96         1.74         7.76 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 
       14.04         9.47        23.24        15.45        11.24         6.97 
TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI 
       18.84        39.95        12.92        23.64        14.83        14.07 
TCGA-SJ-A6ZJ 
       18.28 

  DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE 
                          0.07                           0.13 
  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 
                         20.78                          23.93 
[1] "0.1 - 113.4 (20.8)" "0.1 - 191.8 (23.9)"
[1] "hr=" "1.7"
D87V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 36(16Q22.3) MUTATED                                        67
  DEL PEAK 36(16Q22.3) WILD-TYPE                                     328
                                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                                  79
  DEL PEAK 36(16Q22.3) WILD-TYPE                                33
D87V3, multiclass
                                         clus
vv                                        DEL PEAK 36(16Q22.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           67
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 79
                                         clus
vv                                        DEL PEAK 36(16Q22.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            328
  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"
D87V4, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q22.3) MUTATED    35 119
  DEL PEAK 36(16Q22.3) WILD-TYPE 106 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q22.3) MUTATED     35  119
  DEL PEAK 36(16Q22.3) WILD-TYPE  106  268
     clus
vv    DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE
  NO                            35                            106
  YES                          119                            268
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(16Q22.3) MUTATED    99   9   8  11
  DEL PEAK 36(16Q22.3) WILD-TYPE 264  14   9  24
D87V5, multiclass
    clus
vv   DEL PEAK 36(16Q22.3) MUTATED DEL PEAK 36(16Q22.3) WILD-TYPE
  R0                           99                            264
  R1                            9                             14
  R2                            8                              9
  RX                           11                             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 36(16Q22.3) MUTATED                                  1     2
  DEL PEAK 36(16Q22.3) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 36(16Q22.3) MUTATED                          40
  DEL PEAK 36(16Q22.3) WILD-TYPE                        61
                                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      98
  DEL PEAK 36(16Q22.3) WILD-TYPE   268
D87V6, multiclass
                                           clus
vv                                          DEL PEAK 36(16Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           40
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               98
                                           clus
vv                                          DEL PEAK 36(16Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             61
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  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"
D87V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q22.3) MUTATED     4 112
  DEL PEAK 36(16Q22.3) WILD-TYPE  10 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q22.3) MUTATED      4  112
  DEL PEAK 36(16Q22.3) WILD-TYPE   10  255
                        clus
vv                       DEL PEAK 36(16Q22.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       DEL PEAK 36(16Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            255
[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   131  30
  DEL PEAK 37(16Q23.1) WILD-TYPE 326  39
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                           161                            365 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            30                             39 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-5B-A90C TCGA-A5-A0GG TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       36.69        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        14.43         0.39        29.39        34.16         1.12 
TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AJ-A6NU TCGA-AP-A052 
       22.26        21.21        10.19        16.87        20.78        21.99 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0LF 
       63.91        57.80        45.53        36.89        48.79         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AX-A05U TCGA-AX-A05Y TCGA-AX-A06B TCGA-AX-A06F 
       97.71        46.78        29.69        72.03        53.92        51.09 
TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1C9 TCGA-AX-A1CA 
       28.54        37.78        16.96        13.55        15.25        20.28 
TCGA-AX-A1CC TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 
       12.43        76.83        72.56        25.12        36.39         4.77 
TCGA-AX-A2H4 TCGA-AX-A2H5 TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO 
       30.12        71.24        46.49        19.36         2.96        64.93 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
        0.56        43.82         0.20        20.52         1.38         0.30 
TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JT TCGA-B5-A0K3 TCGA-B5-A0K6 
        0.26         0.30         0.39        43.13        27.29        13.74 
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        29.65        34.95        22.06        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-A0CC TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0TE TCGA-BS-A0TI 
       23.70        10.22        24.13        16.64         4.80        61.87 
TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16J TCGA-D1-A16N 
       49.55        22.55        39.48        27.42        29.92        31.07 
TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A17M TCGA-D1-A17R TCGA-D1-A1NU 
       18.67        14.73        28.08        10.22        11.15        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1O0 TCGA-D1-A3DG TCGA-D1-A3DH 
        0.72        18.25        16.87         2.07         4.27         4.11 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
       16.93        35.38         9.37        31.10       110.10        48.36 
TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       27.32        10.92        37.71        51.42        19.40        34.39 
TCGA-EO-A3AZ TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GK 
       27.16        26.96        22.26        16.34         4.54        22.78 
TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A210 TCGA-EY-A214 
        6.90        17.62        15.09        15.81        12.59        14.40 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR TCGA-EY-A547 
       20.05        29.10        27.35        13.84        11.38        17.92 
TCGA-EY-A54A TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       14.70         5.88        41.06        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        25.02        29.23        41.06        45.01         1.74 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 
        2.43        23.74        13.28        26.10        18.21        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 TCGA-SL-A6JA 
       12.92         7.00         4.44         0.07         0.23 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       41.06        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GH TCGA-A5-A0GI 
       17.85        32.78       112.54       105.37        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-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 TCGA-A5-A2K5 
        7.92        36.33         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-A3BG 
        5.16        10.26        19.79         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 
       18.90         1.68         1.64        14.66        22.49        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       20.81        36.99        20.65        15.62        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW 
       14.76        16.87        22.32        12.82         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N 
       83.67         5.95        23.31        86.07         8.22        23.87 
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        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05W TCGA-AX-A05Z TCGA-AX-A060 
        0.56        13.58        19.82        68.35        46.45        35.34 
TCGA-AX-A062 TCGA-AX-A063 TCGA-AX-A064 TCGA-AX-A06D TCGA-AX-A06H TCGA-AX-A06J 
       45.99        66.58        34.98        12.26        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-A1CE TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CR TCGA-AX-A2H7 
       19.20        20.05        54.12        67.50        11.08        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       61.18        81.37        34.32        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
       31.13         0.23         0.20         1.18        18.35        14.47 
TCGA-B5-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-A0K4 
       32.55        28.64        28.34        30.51        25.91        17.88 
TCGA-B5-A0K7 TCGA-B5-A0K8 TCGA-B5-A0K9 TCGA-B5-A11E TCGA-B5-A11F TCGA-B5-A11H 
       17.10        17.85        11.01         8.71       185.79        88.34 
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-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-A3F9 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH 
       15.29       116.25        96.30        78.81        62.14        14.27 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC 
       35.21        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-A0RY TCGA-BG-A0VV TCGA-BG-A0VX TCGA-BG-A0VZ TCGA-BG-A0W1 
       21.17        15.42        26.66        34.29        52.64        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B TCGA-BG-A220 
       56.58        14.83        14.73        14.01        15.45        14.27 
TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AD TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP 
        1.81         9.57        20.02        20.12        11.31         6.81 
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-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-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-A169 TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E 
       15.72        36.10        37.32        36.36        37.51        36.79 
TCGA-D1-A16I TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       11.51        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-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-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        8.48        44.88         0.26        89.33        10.92        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        16.04         7.36        16.80 
TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       49.15        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3KX 
       51.52        26.43        35.15        17.19        17.88        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        24.36        27.16 
TCGA-EY-A1GH TCGA-EY-A1GI TCGA-EY-A1GJ TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP 
       23.34        23.34        23.90        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        11.08         6.48        19.33 
TCGA-EY-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A548 
       10.19        18.87        22.82        45.76        31.04        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 
       19.89        16.96        40.01        39.88        39.95         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KP-A3W1 
       13.84         8.98        28.96         7.76        14.04         9.47 
TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
       23.24        15.45        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83        14.07        18.28 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.07                           0.13 
  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 
                         21.21                          23.90 
[1] "0.1 - 113.4 (21.2)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2"  
D88V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                        69
  DEL PEAK 37(16Q23.1) WILD-TYPE                                     326
                                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                                  86
  DEL PEAK 37(16Q23.1) WILD-TYPE                                26
D88V3, multiclass
                                         clus
vv                                        DEL PEAK 37(16Q23.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           69
  MIXED SEROUS AND ENDOMETRIOID                                      7
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 86
                                         clus
vv                                        DEL PEAK 37(16Q23.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            326
  MIXED SEROUS AND ENDOMETRIOID                                       14
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D88V4, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    37 125
  DEL PEAK 37(16Q23.1) WILD-TYPE 104 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     37  125
  DEL PEAK 37(16Q23.1) WILD-TYPE  104  262
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                            37                            104
  YES                          125                            262
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(16Q23.1) MUTATED   102   8  11  12
  DEL PEAK 37(16Q23.1) WILD-TYPE 261  15   6  23
D88V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  R0                          102                            261
  R1                            8                             15
  R2                           11                              6
  RX                           12                             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 37(16Q23.1) MUTATED                                  1     3
  DEL PEAK 37(16Q23.1) WILD-TYPE                                3    17
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 37(16Q23.1) MUTATED                          46
  DEL PEAK 37(16Q23.1) WILD-TYPE                        55
                                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      99
  DEL PEAK 37(16Q23.1) WILD-TYPE   267
D88V6, multiclass
                                           clus
vv                                          DEL PEAK 37(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                3
  BLACK OR AFRICAN AMERICAN                                           46
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               99
                                           clus
vv                                          DEL PEAK 37(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 17
  BLACK OR AFRICAN AMERICAN                                             55
  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"
D88V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED     4 118
  DEL PEAK 37(16Q23.1) WILD-TYPE  10 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      4  118
  DEL PEAK 37(16Q23.1) WILD-TYPE   10  249
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            249
[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    91  27
  DEL PEAK 38(17P13.3) WILD-TYPE 366  42
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                           118                            408 
  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                            27                             42 
$`DEL PEAK 38(17P13.3) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A1OG 
       41.06        36.69        65.75        60.53        19.96        11.44 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF 
       28.64         7.33        14.43         0.39        34.16         1.12 
TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW 
       18.90         1.64        17.06        10.19        16.87        16.87 
TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 
       20.78        21.99         5.95        57.80        45.53        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AW-A1PO 
      125.42        36.36        46.78        21.90        36.13         0.56 
TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CR 
       53.92        28.54        37.78        16.96        13.55        11.08 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX 
       61.18        19.36        17.75        64.93         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI 
        0.20        20.52         1.38         0.30         0.26         0.39 
TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11N 
       80.38        27.29        17.85         4.11        75.72        43.96 
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        29.65 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L 
       22.06        36.49        15.45         6.81        10.16        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ 
       16.64        61.87        67.20        49.55        29.95        22.55 
TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16N TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW 
       39.48        37.32        31.07        18.67        13.22         0.72 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A8L9 TCGA-EO-A1Y5 
       16.93        35.38         9.37        31.10        27.32        10.92 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW 
       49.15        37.71        51.42        19.40        22.26        16.34 
TCGA-EY-A1GJ TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 
       23.90         6.90        17.62        15.09        11.08        10.19 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 
       29.10        11.38        17.92        14.70        41.06        39.95 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.93        25.02        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 
       14.04         2.43        23.74        13.28        23.24        23.97 
TCGA-PG-A915 TCGA-PG-A917 TCGA-QS-A8F1 TCGA-SL-A6J9 
        7.00         6.97         4.44         0.07 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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 
       10.26        19.79        29.39         2.40        34.36         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        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       22.32        12.82         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        63.91        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI 
       20.91       117.99       110.37         3.39        63.16        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-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-AX-A05S TCGA-AX-A05T TCGA-AX-A05U 
       10.42        27.85        16.24        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-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-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 
       54.12        67.50        25.12        36.39         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       71.24        40.80        81.37        34.32        46.49        26.33 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G7 
       30.74         2.96        31.13         0.23         0.20         0.30 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
        1.18        18.35        14.47        56.91        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-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-A1MZ TCGA-B5-A3FA 
       50.89        14.40        14.70        11.70        15.29        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       78.81        62.14        14.27        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-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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 
        0.69         3.95         3.65        17.49        19.53         6.64 
TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C 
       30.15        18.02        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M 
       30.44         1.28        28.01        28.08        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-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-D1-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27         4.11        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       23.38        48.36        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
        7.36        16.80        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       57.60        51.52        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       27.16        17.88        26.96        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
       14.99         4.54        53.88        24.36        27.16        23.34 
TCGA-EY-A1GI TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.34        22.78        13.97        19.27        18.84        17.88 
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        20.05        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D 
       27.35        13.84        14.14        19.89        16.96         5.88 
TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU 
       40.01        39.88         7.99        13.84         8.98        96.69 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-KP-A3W1 TCGA-KP-A3W3 
       59.01         9.07        28.96        29.23         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-QF-A5YS TCGA-QF-A5YT 
       18.21        15.45        12.92        11.24        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.83        14.07        18.28         0.23 

  DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE 
                          0.07                           0.13 
  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 
                         20.65                          23.90 
[1] "0.1 - 125.4 (20.6)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.5"
D89V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 38(17P13.3) MUTATED                                        46
  DEL PEAK 38(17P13.3) WILD-TYPE                                     349
                                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                                  64
  DEL PEAK 38(17P13.3) WILD-TYPE                                48
D89V3, multiclass
                                         clus
vv                                        DEL PEAK 38(17P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           46
  MIXED SEROUS AND ENDOMETRIOID                                      9
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 64
                                         clus
vv                                        DEL PEAK 38(17P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            349
  MIXED SEROUS AND ENDOMETRIOID                                       12
  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"
D89V4, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.3) MUTATED    23  96
  DEL PEAK 38(17P13.3) WILD-TYPE 118 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.3) MUTATED     23   96
  DEL PEAK 38(17P13.3) WILD-TYPE  118  291
     clus
vv    DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE
  NO                            23                            118
  YES                           96                            291
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(17P13.3) MUTATED    72   7   4  12
  DEL PEAK 38(17P13.3) WILD-TYPE 291  16  13  23
D89V5, multiclass
    clus
vv   DEL PEAK 38(17P13.3) MUTATED DEL PEAK 38(17P13.3) WILD-TYPE
  R0                           72                            291
  R1                            7                             16
  R2                            4                             13
  RX                           12                             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 38(17P13.3) MUTATED                                  0     2
  DEL PEAK 38(17P13.3) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 38(17P13.3) MUTATED                          37
  DEL PEAK 38(17P13.3) WILD-TYPE                        64
                                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      69
  DEL PEAK 38(17P13.3) WILD-TYPE   297
D89V6, multiclass
                                           clus
vv                                          DEL PEAK 38(17P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           37
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               69
                                           clus
vv                                          DEL PEAK 38(17P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  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"
D89V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(17P13.3) MUTATED     3  85
  DEL PEAK 38(17P13.3) WILD-TYPE  11 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17P13.3) MUTATED      3   85
  DEL PEAK 38(17P13.3) WILD-TYPE   11  282
                        clus
vv                       DEL PEAK 38(17P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 38(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            282
[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    96  27
  DEL PEAK 39(17P11.2) WILD-TYPE 361  42
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                           123                            403 
  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                            27                             42 
$`DEL PEAK 39(17P11.2) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       41.06        36.69        65.75        60.53        36.82        19.96 
TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M 
       11.44        36.33        91.04        28.64         7.33         1.18 
TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ TCGA-AJ-A3I9 
       14.43         0.39         1.12        18.90         1.64        17.06 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
       20.81        21.21        10.19        16.87        16.87        20.78 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J TCGA-AP-A0L8 
        5.95        63.91        57.80        45.53        36.89        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AW-A1PO TCGA-AX-A0IU 
      125.42        36.36        97.71        46.78         0.56        28.54 
TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CF TCGA-AX-A1CR TCGA-AX-A2H2 
       37.78        16.96        13.55        76.83        11.08         4.77 
TCGA-AX-A2H5 TCGA-AX-A2HF TCGA-AX-A2HH TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX 
       71.24        19.36        17.75        64.93         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 
        0.20        20.52         1.38         0.26         0.30         1.18 
TCGA-AX-A3GI TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11N 
        0.39        27.29        17.85         4.11        75.72        43.96 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD 
      102.31        50.89        11.87        12.79       116.25        33.11 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BK-A139 TCGA-BK-A26L TCGA-BK-A4ZD TCGA-BS-A0U9 
       36.49        15.45        10.16        24.13        16.64        67.20 
TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A169 TCGA-D1-A16I TCGA-D1-A16N 
       29.95        22.55        39.48        37.32        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A2G7 TCGA-D1-A3DH 
       18.67        13.22         0.72        18.25        44.88         4.11 
TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A8L9 
       16.93        35.38         9.37        31.10        48.36        27.32 
TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       10.92        49.15        37.71        51.42        19.40        34.39 
TCGA-EO-A3KU TCGA-EY-A1GM TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A4KR 
       22.26         6.90        17.62        11.08        10.19        11.38 
TCGA-EY-A547 TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY 
       17.92        14.70        41.06        39.95         9.07        28.93 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-PG-A5BC TCGA-PG-A7D5 
       14.04         2.43        23.74        13.28        23.24        23.97 
TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
        7.00         4.44         0.07 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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        10.26        19.79        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL 
       34.36        34.16         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        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       14.76        22.32        12.82         2.70         0.13        83.67 
TCGA-AP-A052 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O 
       21.99        23.31        86.07         8.22        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LJ 
       20.91       117.99       110.37         3.39        63.16        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        21.90        36.13        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-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-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        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-A2H4 
       72.56        54.12        67.50        25.12        36.39        30.12 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       40.80        61.18        81.37        34.32        46.49        26.33 
TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G4 
       30.74         2.96        31.13         0.23         0.20         0.30 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       18.35        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-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-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-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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD TCGA-B5-A5OE 
       62.14        14.27        29.65        41.06        34.13        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       22.06        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-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-BG-A3PP TCGA-BK-A0C9 
       20.02        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-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-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-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-A16J TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 
       17.49        19.53         6.64        30.15        18.02        14.73 
TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H 
        1.58         7.00         0.99        30.44         1.28        28.01 
TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.08        26.37        10.22         1.51         1.78        11.15 
TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-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-A2G5 
        2.07        15.06         1.05         3.95         3.52        41.42 
TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        8.48         0.26         4.27        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A2QT TCGA-DI-A2QY 
       16.31        39.29        36.62        24.30        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       16.80        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 
       26.96        16.34        14.53        24.89         6.21        14.99 
TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
        4.54        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GJ TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GO TCGA-EY-A1GP TCGA-EY-A1GQ 
       23.90        22.78        13.97        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-A2ON TCGA-EY-A2OO 
       12.59        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 
       31.04        29.10        27.35        13.84        14.14        19.89 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96         5.88        40.01        39.88         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-KP-A3W1 TCGA-KP-A3W3 
        8.98        96.69        59.01        28.96         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A6IB TCGA-PG-A914 TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS 
       18.21        15.45        12.92        11.24         6.97        18.84 
TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       39.95        12.92        23.64        14.83        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE 
                          0.07                           0.13 
  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 
                         20.52                          23.87 
[1] "0.1 - 125.4 (20.5)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.3"
D90V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 39(17P11.2) MUTATED                                        45
  DEL PEAK 39(17P11.2) WILD-TYPE                                     350
                                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                                  71
  DEL PEAK 39(17P11.2) WILD-TYPE                                41
D90V3, multiclass
                                         clus
vv                                        DEL PEAK 39(17P11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           45
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 71
                                         clus
vv                                        DEL PEAK 39(17P11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            350
  MIXED SEROUS AND ENDOMETRIOID                                       13
  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"
D90V4, binary
                                cls
clus                               0   1
  DEL PEAK 39(17P11.2) MUTATED    26  98
  DEL PEAK 39(17P11.2) WILD-TYPE 115 289
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED     26   98
  DEL PEAK 39(17P11.2) WILD-TYPE  115  289
     clus
vv    DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  NO                            26                            115
  YES                           98                            289
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17P11.2) MUTATED    77   7   4  10
  DEL PEAK 39(17P11.2) WILD-TYPE 286  16  13  25
D90V5, multiclass
    clus
vv   DEL PEAK 39(17P11.2) MUTATED DEL PEAK 39(17P11.2) WILD-TYPE
  R0                           77                            286
  R1                            7                             16
  R2                            4                             13
  RX                           10                             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 39(17P11.2) MUTATED                                  0     2
  DEL PEAK 39(17P11.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 39(17P11.2) MUTATED                          36
  DEL PEAK 39(17P11.2) WILD-TYPE                        65
                                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      77
  DEL PEAK 39(17P11.2) WILD-TYPE   289
D90V6, multiclass
                                           clus
vv                                          DEL PEAK 39(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           36
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               77
                                           clus
vv                                          DEL PEAK 39(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             65
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                289
[1] 5 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  87
  DEL PEAK 39(17P11.2) WILD-TYPE  11 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17P11.2) MUTATED      3   87
  DEL PEAK 39(17P11.2) WILD-TYPE   11  280
                        clus
vv                       DEL PEAK 39(17P11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           87
                        clus
vv                       DEL PEAK 39(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            280
[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    80  20
  DEL PEAK 40(17Q11.2) WILD-TYPE 377  49
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                           100                            426 
  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                            20                             49 
$`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        14.43         0.39        29.39        18.90 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A052 
       22.26        17.06        20.81        10.19        16.87        21.99 
TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI 
       63.91        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 
       46.78         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        64.93         0.56 
TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 
       43.82         0.20        20.52         1.38         0.26         0.30 
TCGA-B5-A11N TCGA-B5-A1MS TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD 
       43.96       102.31        12.79       116.25        33.11        34.13 
TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A139 TCGA-BK-A26L 
       22.06        36.49        15.45         6.81        10.16        24.13 
TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZZ TCGA-D1-A169 
       16.64        61.87        67.20        49.55        22.55        37.32 
TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW 
       11.51        31.07        14.73        28.08        13.22         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QU TCGA-E6-A1LZ TCGA-E6-A8L9 
        2.07         4.11         9.37        31.10        48.36        27.32 
TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS 
       16.80        49.15        37.71        51.42        19.40        34.39 
TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GW TCGA-EY-A212 
       22.26        16.34         4.54        23.90        11.08        10.19 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EW 
       29.10        13.84        17.92        41.06        39.95        59.01 
TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3VZ TCGA-KP-A3W0 
       25.02        29.23         1.74         7.76        23.74        13.28 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A8F1 
       26.10        23.97        12.92         4.44 

$`DEL PEAK 40(17Q11.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 
       41.06        36.69        10.29       106.88       149.56        37.02 
TCGA-A5-A0G9 TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG 
       83.51        17.85        32.78       112.54       105.37        87.32 
TCGA-A5-A0GH TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       74.10        57.53        60.53        46.55        38.37        36.82 
TCGA-A5-A0GU TCGA-A5-A0GV TCGA-A5-A0GW TCGA-A5-A0GX TCGA-A5-A0R8 TCGA-A5-A0R9 
       28.27        20.81        23.21        68.65        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-A3LP 
       91.04        46.32        28.64         5.33         5.16        14.96 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF 
       10.26        19.79         2.40        34.36        34.16         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
        0.76         1.68         1.64        14.66        22.49        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NF TCGA-AJ-A3NG TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J 
       83.67         5.95        23.31        86.07         8.22        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF 
       23.87        12.20        20.91       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-A3K1 
        6.71        30.90        10.42        27.85        16.24        21.90 
TCGA-AP-A5FX TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
       36.13        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-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI 
       16.96        15.25        20.28        12.43        20.05        72.56 
TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H7 
       54.12        67.50        25.12        36.39         4.77        40.80 
TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       81.37        34.32        46.49        26.33        17.75        30.74 
TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3G4 TCGA-AX-A3G8 
        2.96        31.13         0.23         0.20         0.30         1.18 
TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS 
       18.35        14.47         0.39        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        27.29        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-A11O 
      113.36        88.34        75.72        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-A1MY TCGA-B5-A1MZ TCGA-B5-A3FA 
       14.40        14.70        11.70        11.87        15.29        96.30 
TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       78.81        62.14        14.27        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        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-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        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       23.70        20.12        11.31        35.90        34.98         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-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-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-A16O 
       36.36        37.51        36.79        27.42        29.92        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y 
       10.65         0.69        18.67         3.95         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A TCGA-D1-A17B 
       19.53         6.64        30.15        18.02         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M 
        0.99        30.44         1.28        28.01        26.37        10.22 
TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U 
        1.51         1.78        11.15        24.30         2.33        22.92 
TCGA-D1-A1NS TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
        1.41        18.25        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27        16.93        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QT TCGA-DI-A2QY 
       39.29        36.62        24.30        35.38        12.39       110.10 
TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ TCGA-EC-A1QX 
       23.38        17.06         2.37         6.67        16.04         7.36 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 
       51.52        26.43        35.15        17.19        27.16        17.88 
TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD 
       26.96        14.53        24.89         6.21        14.99        53.88 
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-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        11.38        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.88        40.01        39.88         7.99        13.84         8.98 
TCGA-FI-A2EU TCGA-FI-A2EX TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A3PV TCGA-FI-A3PX 
       96.69         9.07        28.93        28.96        41.06        45.01 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       14.04         2.43         9.47        18.21        23.24        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       23.64        14.83        14.07        18.28         0.07         0.23 

  DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE 
                          0.20                           0.07 
  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 
                        22.260                         23.425 
[1] "0.2 - 125.4 (22.3)" "0.1 - 191.8 (23.4)"
[1] "hr=" "1.8"
D91V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 40(17Q11.2) MUTATED                                        43
  DEL PEAK 40(17Q11.2) WILD-TYPE                                     352
                                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                                  53
  DEL PEAK 40(17Q11.2) WILD-TYPE                                59
D91V3, multiclass
                                         clus
vv                                        DEL PEAK 40(17Q11.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           43
  MIXED SEROUS AND ENDOMETRIOID                                      5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 53
                                         clus
vv                                        DEL PEAK 40(17Q11.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            352
  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"
D91V4, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED    21  80
  DEL PEAK 40(17Q11.2) WILD-TYPE 120 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED     21   80
  DEL PEAK 40(17Q11.2) WILD-TYPE  120  307
     clus
vv    DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  NO                            21                            120
  YES                           80                            307
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17Q11.2) MUTATED    65   6   6   7
  DEL PEAK 40(17Q11.2) WILD-TYPE 298  17  11  28
D91V5, multiclass
    clus
vv   DEL PEAK 40(17Q11.2) MUTATED DEL PEAK 40(17Q11.2) WILD-TYPE
  R0                           65                            298
  R1                            6                             17
  R2                            6                             11
  RX                            7                             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 40(17Q11.2) MUTATED                                  0     2
  DEL PEAK 40(17Q11.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 40(17Q11.2) MUTATED                          21
  DEL PEAK 40(17Q11.2) WILD-TYPE                        80
                                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      68
  DEL PEAK 40(17Q11.2) WILD-TYPE   298
D91V6, multiclass
                                           clus
vv                                          DEL PEAK 40(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           21
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            2
  WHITE                                                               68
                                           clus
vv                                          DEL PEAK 40(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             80
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              7
  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"
D91V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17Q11.2) MUTATED     3  70
  DEL PEAK 40(17Q11.2) WILD-TYPE  11 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17Q11.2) MUTATED      3   70
  DEL PEAK 40(17Q11.2) WILD-TYPE   11  297
                        clus
vv                       DEL PEAK 40(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           70
                        clus
vv                       DEL PEAK 40(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                 11
  NOT HISPANIC OR LATINO                            297
[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    82  26
  DEL PEAK 41(17Q21.31) WILD-TYPE 375  43
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                            108                             418 
  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                             26                              43 
$`DEL PEAK 41(17Q21.31) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R7 TCGA-A5-A1OG 
       41.06        36.69        65.75        60.53        17.59        11.44 
TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A2QM 
       91.04         7.33         1.18        14.43         0.39        29.39 
TCGA-AJ-A3BI TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3NH 
       18.90        22.26        17.06        20.81        21.21        10.19 
TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       16.87        21.99         5.95        63.91        57.80        45.53 
TCGA-AP-A05J TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX 
       36.89        48.79       125.42        97.71        46.78        36.13 
TCGA-AW-A1PO TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CP TCGA-AX-A2H4 TCGA-AX-A2H5 
        0.56        16.96        13.55        36.39        30.12        71.24 
TCGA-AX-A2H8 TCGA-AX-A2IO TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ TCGA-AX-A3G1 
       61.18        64.93         0.56        43.82         0.20        20.52 
TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11N 
        1.38         0.30        27.29        17.85         4.11        43.96 
TCGA-B5-A1MS TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 TCGA-B5-A5OD TCGA-BG-A0M6 
      102.31       116.25        33.11        29.65        34.13        22.06 
TCGA-BG-A0M8 TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BK-A4ZD 
       36.49        15.45         6.81        10.22        24.13        16.64 
TCGA-BS-A0U9 TCGA-BS-A0V8 TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A169 TCGA-D1-A16I 
       67.20        49.55        29.95        22.55        37.32        11.51 
TCGA-D1-A16N TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NX TCGA-D1-A1O0 
       31.07        14.73        28.08        13.22        18.25         2.07 
TCGA-D1-A3DH TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A8L9 TCGA-EO-A1Y7 
        4.11         9.37        12.39        31.10        27.32        49.15 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3KU TCGA-EO-A3KW 
       37.71        51.42        19.40        34.39        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A212 
        4.54        23.90        17.62        11.08        12.59        10.19 
TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       29.10        11.38        17.92        41.06        39.95        96.69 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       28.93        25.02         1.74         7.76         2.43        23.74 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A7D5 TCGA-PG-A914 TCGA-QS-A8F1 
       13.28        26.10        18.21        23.97        12.92         4.44 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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        10.26 
TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79         2.40        34.36        34.16         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-A5DV 
       15.62        15.35        15.95        14.76        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A054 
       12.82        20.78         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        23.87        12.20        20.91       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-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-A05W 
       16.24        21.90        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-A1C9 TCGA-AX-A1CA TCGA-AX-A1CC TCGA-AX-A1CE 
       13.28        19.20        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-A1CR 
       76.83        72.56        54.12        67.50        25.12        11.08 
TCGA-AX-A2H2 TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
        4.77        40.80        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN TCGA-AX-A3FS 
       26.33        17.75        30.74         2.96        31.13         0.23 
TCGA-AX-A3FT TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.20         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-A11I TCGA-B5-A11J TCGA-B5-A11L 
      185.79       113.36        88.34        75.72        54.44        45.90 
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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A5OC 
       12.79        96.30        78.81        62.14        14.27        41.06 
TCGA-B5-A5OE TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.95        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       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-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 
       20.02        23.70        20.12        11.31        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A56F TCGA-BK-A6W3 
        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-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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X 
       33.63        10.65         0.69        18.67         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-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-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27        16.93        89.33        10.92        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       110.10 
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        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        10.92        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       46.26        57.60        51.52        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       27.16        17.88        26.96        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-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-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP 
       14.40        18.87        22.82        20.05        45.76        31.04 
TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 
       27.35        13.84        14.14        19.89        14.70        16.96 
TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
        5.88        40.01        39.88         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
       59.01         9.07        28.96        29.23        41.06        45.01 
TCGA-K6-A3WQ TCGA-KP-A3W1 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A915 TCGA-PG-A916 
       14.04         9.47        23.24        15.45         7.00        11.24 
TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 
        6.97        18.84        39.95        12.92        23.64        14.83 
TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.07        18.28         0.07         0.23 

  DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE 
                           0.20                            0.07 
  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 
                         22.260                          23.425 
[1] "0.2 - 125.4 (22.3)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.4"
D92V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 41(17Q21.31) MUTATED                                        44
  DEL PEAK 41(17Q21.31) WILD-TYPE                                     351
                                 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                                  60
  DEL PEAK 41(17Q21.31) WILD-TYPE                                52
D92V3, multiclass
                                         clus
vv                                        DEL PEAK 41(17Q21.31) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            44
  MIXED SEROUS AND ENDOMETRIOID                                       5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  60
                                         clus
vv                                        DEL PEAK 41(17Q21.31) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             351
  MIXED SEROUS AND ENDOMETRIOID                                        16
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D92V4, binary
                                 cls
clus                                0   1
  DEL PEAK 41(17Q21.31) MUTATED    21  88
  DEL PEAK 41(17Q21.31) WILD-TYPE 120 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(17Q21.31) MUTATED     21   88
  DEL PEAK 41(17Q21.31) WILD-TYPE  120  299
     clus
vv    DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE
  NO                             21                             120
  YES                            88                             299
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 41(17Q21.31) MUTATED    66   6   6  11
  DEL PEAK 41(17Q21.31) WILD-TYPE 297  17  11  24
D92V5, multiclass
    clus
vv   DEL PEAK 41(17Q21.31) MUTATED DEL PEAK 41(17Q21.31) WILD-TYPE
  R0                            66                             297
  R1                             6                              17
  R2                             6                              11
  RX                            11                              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 41(17Q21.31) MUTATED                                  1     2
  DEL PEAK 41(17Q21.31) WILD-TYPE                                3    18
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 41(17Q21.31) MUTATED                          27
  DEL PEAK 41(17Q21.31) WILD-TYPE                        74
                                 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      68
  DEL PEAK 41(17Q21.31) WILD-TYPE   298
D92V6, multiclass
                                           clus
vv                                          DEL PEAK 41(17Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 2
  BLACK OR AFRICAN AMERICAN                                            27
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             3
  WHITE                                                                68
                                           clus
vv                                          DEL PEAK 41(17Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  18
  BLACK OR AFRICAN AMERICAN                                              74
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               6
  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"
D92V7, binary
                                 cls
clus                                0   1
  DEL PEAK 41(17Q21.31) MUTATED     6  73
  DEL PEAK 41(17Q21.31) WILD-TYPE   8 294
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(17Q21.31) MUTATED      6   73
  DEL PEAK 41(17Q21.31) WILD-TYPE    8  294
                        clus
vv                       DEL PEAK 41(17Q21.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            73
                        clus
vv                       DEL PEAK 41(17Q21.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             294
[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    75  13
  DEL PEAK 42(18Q21.2) WILD-TYPE 382  56
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            88                            438 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            13                             56 
$`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 
       29.39        34.16         1.12        21.21        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         1.38 
TCGA-AX-A3G4 TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A11H TCGA-B5-A11P 
        0.30         0.30         0.39        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         3.95        28.08         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ 
        2.07         4.11        16.93        31.10       110.10        48.36 
TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GC TCGA-EY-A1GO 
       49.15        37.71        51.42        27.16         4.54        19.27 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A2OO 
       18.84        15.09        11.08        14.40        20.05        45.76 
TCGA-EY-A3QX TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EX TCGA-FI-A2EY 
       13.84        17.92         5.88        41.06         9.07        28.93 
TCGA-FI-A3PX TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
       45.01        14.04         2.43        23.74        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.24        23.97         4.44         0.07 

$`DEL PEAK 42(18Q21.2) WILD-TYPE`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 
       41.06        36.69        10.29       106.88       149.56        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        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-A1OH TCGA-A5-A1OJ TCGA-A5-A1OK 
       42.35        15.95         7.92        36.33         9.60         8.02 
TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23N TCGA-AJ-A23O TCGA-AJ-A2QL 
       91.04         5.33         5.16        14.43        10.26        19.79 
TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ 
        2.40        34.36         0.76        18.90         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        17.06        20.81        36.99 
TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL 
       20.65        15.62        10.19        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT 
       16.87        16.87        22.32        12.82        20.78         2.70 
TCGA-AJ-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        63.91        57.80        36.89        23.87        12.20 
TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LG TCGA-AP-A0LJ 
       20.91        48.79       117.99       110.37        63.16        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        46.78        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        21.90        36.13         0.56 
TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y TCGA-AX-A05Z 
       13.58        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-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-A1CI TCGA-AX-A1CJ 
       13.55        15.25        12.43        20.05        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        40.80 
TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG 
       61.18        81.37        34.32        46.49        19.36        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT 
       17.75        30.74        31.13        64.93         0.23         0.20 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        0.56        43.82         0.26         1.18        18.35        14.47 
TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV TCGA-B5-A0JX 
       56.91        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        27.29 
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-A11I TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79       113.36        75.72        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-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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       15.29        96.30        78.81        62.14        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        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-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98         6.21        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-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-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-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        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        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-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-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.27        89.33        10.92        27.16        16.31        39.29 
TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-E6-A1LX 
       36.62        24.30        35.38         9.37        12.39        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        27.32        16.04         7.36 
TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       16.80        10.92        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       17.19        17.88        26.96        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
       24.89         6.21        14.99        53.88        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-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-A212 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
       19.33        12.59        10.19        18.87        22.82        31.04 
TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       29.10        27.35        11.38        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96        40.01        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 
        8.98        96.69        59.01        28.96        25.02        29.23 
TCGA-FI-A3PV TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       41.06         1.74         7.76        26.10        18.21        15.45 
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 TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.83        14.07        18.28         0.23 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                          0.07                           0.13 
  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 
                        19.660                         23.755 
[1] "0.1 - 125.4 (19.7)" "0.1 - 191.8 (23.8)"
[1] "hr=" "1.3"
D93V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                                        37
  DEL PEAK 42(18Q21.2) WILD-TYPE                                     358
                                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                                  46
  DEL PEAK 42(18Q21.2) WILD-TYPE                                66
D93V3, multiclass
                                         clus
vv                                        DEL PEAK 42(18Q21.2) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           37
  MIXED SEROUS AND ENDOMETRIOID                                      6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 46
                                         clus
vv                                        DEL PEAK 42(18Q21.2) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            358
  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"
D93V4, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED    13  76
  DEL PEAK 42(18Q21.2) WILD-TYPE 128 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED     13   76
  DEL PEAK 42(18Q21.2) WILD-TYPE  128  311
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  NO                            13                            128
  YES                           76                            311
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q21.2) MUTATED    51   5   5   8
  DEL PEAK 42(18Q21.2) WILD-TYPE 312  18  12  27
D93V5, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  R0                           51                            312
  R1                            5                             18
  R2                            5                             12
  RX                            8                             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 42(18Q21.2) MUTATED                                  0     2
  DEL PEAK 42(18Q21.2) WILD-TYPE                                4    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 42(18Q21.2) MUTATED                          25
  DEL PEAK 42(18Q21.2) WILD-TYPE                        76
                                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      54
  DEL PEAK 42(18Q21.2) WILD-TYPE   312
D93V6, multiclass
                                           clus
vv                                          DEL PEAK 42(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     0
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           25
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               54
                                           clus
vv                                          DEL PEAK 42(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       4
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             76
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  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"
D93V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED     4  64
  DEL PEAK 42(18Q21.2) WILD-TYPE  10 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED      4   64
  DEL PEAK 42(18Q21.2) WILD-TYPE   10  303
                        clus
vv                       DEL PEAK 42(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       DEL PEAK 42(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 10
  NOT HISPANIC OR LATINO                            303
[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    75  19
  DEL PEAK 43(18Q23) WILD-TYPE 382  50
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          94                          432 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          19                           50 
$`DEL PEAK 43(18Q23) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0G5 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 
       41.06        37.02        65.75        60.53        36.82        19.96 
TCGA-A5-A0R7 TCGA-A5-A1OG TCGA-A5-A1OH TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO 
       17.59        11.44        36.33        46.32        28.64         7.33 
TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A2QK TCGA-AJ-A3BD TCGA-AJ-A3BF 
       14.96         1.18        14.43         0.39        34.16         1.12 
TCGA-AJ-A3IA TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A052 TCGA-AP-A05H TCGA-AP-A0LF 
       20.81        21.21        16.87        21.99        45.53         3.39 
TCGA-AP-A0LH TCGA-AP-A0LI TCGA-AX-A0IU TCGA-AX-A1CA TCGA-AX-A1CR TCGA-AX-A2H2 
       36.36        97.71        28.54        20.28        11.08         4.77 
TCGA-AX-A2H4 TCGA-AX-A2HK TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 
       30.12         2.96         0.20        20.52         1.38         0.30 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JX TCGA-B5-A11E TCGA-B5-A11P 
        0.30         0.39        80.38        44.71         8.71        36.82 
TCGA-B5-A1MY TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A2AE 
       11.87       116.25        33.11        34.95        15.45        23.70 
TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A139 TCGA-BK-A4ZD TCGA-BS-A0TI TCGA-BS-A0U9 
        6.81        10.22        10.16        16.64        61.87        67.20 
TCGA-BS-A0V8 TCGA-D1-A169 TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NW 
       49.55        37.32        18.67         3.95        28.08         0.72 
TCGA-D1-A1O0 TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
        2.07         4.11        16.93        12.39        31.10       110.10 
TCGA-E6-A1LZ TCGA-EO-A1Y7 TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EY-A1GC 
       48.36        49.15        37.71        51.42        27.16         4.54 
TCGA-EY-A1GP TCGA-EY-A1GS TCGA-EY-A1GW TCGA-EY-A212 TCGA-EY-A2ON TCGA-EY-A2OO 
       18.84        15.09        11.08        10.19        20.05        45.76 
TCGA-EY-A2OQ TCGA-EY-A3QX TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX 
       29.10        13.84         5.88        41.06        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 
       28.93        25.02        14.04         2.43        23.74        13.28 
TCGA-KP-A3W1 TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
        9.47        23.97         4.44         0.07 

$`DEL PEAK 43(18Q23) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       106.88       149.56        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-A1OJ TCGA-A5-A1OK TCGA-A5-A2K2 TCGA-A5-A2K5 TCGA-A5-A2K7 
        7.92         9.60         8.02        91.04         5.33         5.16 
TCGA-AJ-A23O TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BG 
       10.26        19.79        29.39         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         1.68         1.64        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ 
       17.06        36.99        20.65        15.62        10.19        15.35 
TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU 
       15.95        14.76        16.87        22.32        12.82        20.78 
TCGA-AJ-A8CT TCGA-AJ-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        63.91        57.80        36.89        23.87        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-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        46.78        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        21.90        36.13 
TCGA-AW-A1PO TCGA-AX-A05S TCGA-AX-A05T TCGA-AX-A05U TCGA-AX-A05W TCGA-AX-A05Y 
        0.56        13.58        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-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-A2H5 
       72.56        54.12        67.50        25.12        36.39        71.24 
TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF 
       40.80        61.18        81.37        34.32        46.49        19.36 
TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS 
       26.33        17.75        30.74        31.13        64.93         0.23 
TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20         0.56        43.82         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        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        27.29 
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-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-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-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-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       12.79        96.30        78.81        62.14        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        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-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        20.02        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L 
       35.90        34.98         6.21        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-A0TJ TCGA-BS-A0U5 TCGA-BS-A0U7 
       78.21         4.80        77.95        67.99        96.49        30.74 
TCGA-BS-A0U8 TCGA-BS-A0UA TCGA-BS-A0UF TCGA-BS-A0UJ TCGA-BS-A0UL TCGA-BS-A0UT 
       97.41        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-A168 TCGA-D1-A16B TCGA-D1-A16D 
       32.58         0.66        15.72        36.10        36.36        37.51 
TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J TCGA-D1-A16N TCGA-D1-A16O 
       36.79        27.42        11.51        29.92        31.07        33.63 
TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-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        14.73         1.58         7.00         0.99 
TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N 
       30.44         1.28        28.01        26.37        10.22         1.51 
TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS 
        1.78        11.15        24.30         2.33        22.92         1.41 
TCGA-D1-A1NU TCGA-D1-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-A3DA 
        3.95         3.52        41.42         8.48        44.88         0.26 
TCGA-D1-A3DG TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU 
        4.27        89.33        10.92        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        27.32        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X 
       10.92        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       17.88        26.96        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        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-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-A214 TCGA-EY-A215 TCGA-EY-A2OM TCGA-EY-A2OP 
       19.33        12.59        14.40        18.87        22.82        31.04 
TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       27.35        11.38        17.92        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 
       16.96        40.01        39.88        39.95         7.99        13.84 
TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX 
        8.98        96.69        28.96        29.23        41.06        45.01 
TCGA-H5-A2HR TCGA-JU-AAVI TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
        1.74         7.76        26.10        18.21        23.24        15.45 
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 TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.83        14.07        18.28         0.23 

  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                        0.07                         0.13 
  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 
                      20.005                       23.885 
[1] "0.1 - 116.2 (20.0)" "0.1 - 191.8 (23.9)"
[1] "hr=" "2.1"
D94V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                        37
  DEL PEAK 43(18Q23) WILD-TYPE                                     358
                              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                                  52
  DEL PEAK 43(18Q23) WILD-TYPE                                60
D94V3, multiclass
                                         clus
vv                                        DEL PEAK 43(18Q23) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         37
  MIXED SEROUS AND ENDOMETRIOID                                    6
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               52
                                         clus
vv                                        DEL PEAK 43(18Q23) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          358
  MIXED SEROUS AND ENDOMETRIOID                                     15
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D94V4, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED    12  83
  DEL PEAK 43(18Q23) WILD-TYPE 129 304
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED     12   83
  DEL PEAK 43(18Q23) WILD-TYPE  129  304
     clus
vv    DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  NO                          12                          129
  YES                         83                          304
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 43(18Q23) MUTATED    56   5   8   7
  DEL PEAK 43(18Q23) WILD-TYPE 307  18   9  28
D94V5, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  R0                         56                          307
  R1                          5                           18
  R2                          8                            9
  RX                          7                           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 43(18Q23) MUTATED                                  1     2
  DEL PEAK 43(18Q23) WILD-TYPE                                3    18
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 43(18Q23) MUTATED                          26
  DEL PEAK 43(18Q23) WILD-TYPE                        75
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 43(18Q23) MUTATED                                           3    57
  DEL PEAK 43(18Q23) WILD-TYPE                                         6   309
D94V6, multiclass
                                           clus
vv                                          DEL PEAK 43(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              2
  BLACK OR AFRICAN AMERICAN                                         26
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          3
  WHITE                                                             57
                                           clus
vv                                          DEL PEAK 43(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               18
  BLACK OR AFRICAN AMERICAN                                           75
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            6
  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"
D94V7, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     5  65
  DEL PEAK 43(18Q23) WILD-TYPE   9 302
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      5   65
  DEL PEAK 43(18Q23) WILD-TYPE    9  302
                        clus
vv                       DEL PEAK 43(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                         65
                        clus
vv                       DEL PEAK 43(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          302
[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   115  35
  DEL PEAK 44(19P13.3) WILD-TYPE 342  34
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           150                            376 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            35                             34 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A1OG 
       41.06        36.69        60.53        36.82        19.96        11.44 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A2K3 TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-A5-A3LP 
       36.33        91.04        46.32        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        14.43         0.39        29.39        34.16         1.12 
TCGA-AJ-A3EJ TCGA-AJ-A3EM TCGA-AJ-A3NF TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A6NU 
        1.64        22.26        21.21        16.87        16.87        20.78 
TCGA-AP-A052 TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       21.99         5.95        63.91        57.80        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LF TCGA-AP-A1DQ TCGA-AP-A3K1 TCGA-AP-A5FX 
       48.79       125.42         3.39        46.78        21.90        36.13 
TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA 
       53.92        28.54        37.78        16.96        13.55        20.28 
TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H5 
       76.83        36.39        11.08         4.77        30.12        71.24 
TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO TCGA-AX-A3FX TCGA-AX-A3FZ 
       61.18        19.36         2.96        64.93        43.82         0.20 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3GI TCGA-B5-A0JN 
       20.52         1.38         0.30         0.26         0.39        80.38 
TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
       27.29        17.85         4.11        75.72        36.82       102.31 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A3S1 
       50.89        11.87        12.79       116.25        33.11        29.65 
TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0YV 
       34.13        34.95        22.06        36.49        21.17        12.56 
TCGA-BG-A18C TCGA-BG-A3PP TCGA-BK-A0CC TCGA-BK-A26L TCGA-BS-A0U9 TCGA-BS-A0V8 
       15.45         6.81        10.22        24.13        67.20        49.55 
TCGA-D1-A0ZP TCGA-D1-A0ZZ TCGA-D1-A15V TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16N 
       29.95        22.55        39.48        27.42        11.51        31.07 
TCGA-D1-A16S TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
       18.67        14.73        28.08        13.22         0.72        18.25 
TCGA-D1-A1O0 TCGA-D1-A2G7 TCGA-D1-A3DG TCGA-D1-A3JP TCGA-DI-A1NN TCGA-DI-A1NO 
        2.07        44.88         4.27        16.93        35.38         9.37 
TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LZ TCGA-E6-A8L9 TCGA-EO-A1Y5 
       12.39        31.10       110.10        48.36        27.32        10.92 
TCGA-EO-A1Y8 TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EY-A1GC 
       37.71        51.42        19.40        22.26        16.34         4.54 
TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GV TCGA-EY-A1GW 
       23.90        18.84        17.62        15.09        15.81        11.08 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2ON TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A4KR 
       10.19        14.40        20.05        27.35        13.84        11.38 
TCGA-EY-A54A TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EW TCGA-FI-A2EX 
       14.70        41.06        39.95        96.69        59.01         9.07 
TCGA-FI-A2EY TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR 
       28.93        25.02        29.23        41.06        45.01         1.74 
TCGA-JU-AAVI TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 
        7.76        14.04         2.43        23.74        13.28         9.47 
TCGA-PG-A5BC TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 TCGA-QS-A8F1 TCGA-SL-A6J9 
       23.24        23.97        12.92         7.00         4.44         0.07 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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        10.26        19.79         2.40        34.36         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3I9 TCGA-AJ-A3IA 
       18.90         1.68        14.66        22.49        17.06        20.81 
TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK 
       36.99        20.65        15.62        10.19        15.35        15.95 
TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       14.76        22.32        12.82         2.70         0.13        83.67 
TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       23.31        86.07         8.22        23.87        12.20        20.91 
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-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-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-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-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       15.25        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG 
       25.12        40.80        81.37        34.32        46.49        26.33 
TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW 
       17.75        30.74        31.13         0.23         0.20         0.56 
TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS 
        0.30         1.18        18.35        14.47        56.91        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-A3FH TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX 
       78.81        62.14        14.27        41.06        18.61        20.19 
TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 
       19.33        20.94        35.21        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-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-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-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        20.02        23.70        20.12        11.31        35.90 
TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A4ZD 
       34.98         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-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-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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16V TCGA-D1-A16X 
       29.92        33.63        10.65         0.69         3.95         3.65 
TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A17A 
       17.49        19.53         6.64        30.15        18.02         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O5 TCGA-D1-A1O7 
       22.92         1.41        16.87        18.02        15.06         1.05 
TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-A2G5 TCGA-D1-A2G6 TCGA-D1-A3DA TCGA-D1-A3DH 
        3.95         3.52        41.42         8.48         0.26         4.11 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-E6-A1LX TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 TCGA-EC-A1NJ 
       24.30        23.38        17.06         2.37         6.67        16.04 
TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y7 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T 
        7.36        16.80        49.15        61.74        61.55        66.90 
TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       46.26        57.60        51.52        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 
       17.19        27.16        17.88        26.96        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH 
        6.21        14.99        53.88        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-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-A547 TCGA-EY-A548 
       22.82        45.76        31.04        29.10        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 
       19.89        16.96         5.88        40.01        39.88         7.99 
TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2F4 TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A6IB 
       13.84         8.98        28.96        26.10        18.21        15.45 
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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       14.83        14.07        18.28         0.23 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.07                           0.13 
  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 
                        21.945                         23.785 
[1] "0.1 - 125.4 (21.9)" "0.1 - 191.8 (23.8)"
[1] "hr=" "2.8"
D95V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                        45
  DEL PEAK 44(19P13.3) WILD-TYPE                                     350
                                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                                  98
  DEL PEAK 44(19P13.3) WILD-TYPE                                14
D95V3, multiclass
                                         clus
vv                                        DEL PEAK 44(19P13.3) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           45
  MIXED SEROUS AND ENDOMETRIOID                                      8
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 98
                                         clus
vv                                        DEL PEAK 44(19P13.3) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            350
  MIXED SEROUS AND ENDOMETRIOID                                       13
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   14
[1] 3 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    32 119
  DEL PEAK 44(19P13.3) WILD-TYPE 109 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     32  119
  DEL PEAK 44(19P13.3) WILD-TYPE  109  268
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                            32                            109
  YES                          119                            268
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED    90   9   9  15
  DEL PEAK 44(19P13.3) WILD-TYPE 273  14   8  20
D95V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                           90                            273
  R1                            9                             14
  R2                            9                              8
  RX                           15                             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 44(19P13.3) MUTATED                                  1     2
  DEL PEAK 44(19P13.3) WILD-TYPE                                3    18
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 44(19P13.3) MUTATED                          46
  DEL PEAK 44(19P13.3) WILD-TYPE                        55
                                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      90
  DEL PEAK 44(19P13.3) WILD-TYPE   276
D95V6, multiclass
                                           clus
vv                                          DEL PEAK 44(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                2
  BLACK OR AFRICAN AMERICAN                                           46
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            3
  WHITE                                                               90
                                           clus
vv                                          DEL PEAK 44(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 18
  BLACK OR AFRICAN AMERICAN                                             55
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              6
  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"
D95V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     6 104
  DEL PEAK 44(19P13.3) WILD-TYPE   8 263
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      6  104
  DEL PEAK 44(19P13.3) WILD-TYPE    8  263
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            263
[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    45  12
  DEL PEAK 45(19P12) WILD-TYPE 412  57
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          57                          469 
  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                          12                           57 
$`DEL PEAK 45(19P12) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GN TCGA-A5-A3LO TCGA-AJ-A2QM TCGA-AJ-A3BD TCGA-AJ-A3EJ 
       41.06        60.53         7.33        29.39        34.16         1.64 
TCGA-AJ-A3NF TCGA-AJ-A3TW TCGA-AP-A05D TCGA-AP-A3K1 TCGA-AP-A5FX TCGA-AX-A1C7 
       21.21        16.87        57.80        21.90        36.13        16.96 
TCGA-AX-A1CA TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK TCGA-AX-A3FZ 
       20.28        76.83         4.77        71.24         2.96         0.20 
TCGA-AX-A3G7 TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JZ TCGA-B5-A11P TCGA-B5-A1MS 
        0.30         0.39        80.38        28.64        36.82       102.31 
TCGA-B5-A1MU TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD TCGA-B5-A5OE TCGA-BG-A0M6 
       50.89       116.25        33.11        34.13        34.95        22.06 
TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A3PP TCGA-BS-A0TI TCGA-BS-A0U9 TCGA-D1-A16N 
       12.56        15.45         6.81        61.87        67.20        31.07 
TCGA-D1-A3JP TCGA-DI-A2QT TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3B1 TCGA-EY-A1GV 
       16.93        12.39        49.15        51.42        26.96        15.81 
TCGA-EY-A1GW TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A4KR TCGA-EY-A54A TCGA-EY-A72D 
       11.08        14.40        29.10        11.38        14.70         5.88 
TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EX TCGA-FI-A2EY TCGA-KP-A3VZ TCGA-KP-A3W1 
       41.06        39.95         9.07        28.93        23.74         9.47 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-PG-A914 
       26.10        23.97        12.92 

$`DEL PEAK 45(19P12) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GJ TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GR 
       57.53        65.75        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-A23N 
       28.64         5.33         5.16        14.96         1.18        14.43 
TCGA-AJ-A23O TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF 
       10.26         0.39        19.79         2.40        34.36         1.12 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
        0.76        18.90         1.68        14.66        22.49        22.26 
TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NC TCGA-AJ-A3NE TCGA-AJ-A3NG TCGA-AJ-A3NH 
       17.06        20.81        36.99        20.65        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW 
       15.35        15.95        14.76        16.87        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A053 
       20.78         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        63.91        45.53        36.89 
TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LD 
       23.87        12.20        20.91        48.79       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        46.78        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-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-A1C8 TCGA-AX-A1C9 
       40.11        65.88        13.28        19.20        13.55        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-A1CP TCGA-AX-A1CR TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA 
       36.39        11.08        30.12        40.80        61.18        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       34.32        46.49        19.36        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G8 TCGA-AX-A3G9 
       20.52         1.38         0.30         0.26         1.18        18.35 
TCGA-AX-A3GB TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU TCGA-B5-A0JV 
       14.47        56.91        46.75        43.13        48.76        40.67 
TCGA-B5-A0JX TCGA-B5-A0JY TCGA-B5-A0K0 TCGA-B5-A0K1 TCGA-B5-A0K2 TCGA-B5-A0K3 
       44.71        32.55        28.34        30.51        25.91        27.29 
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-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-A1MY TCGA-B5-A1MZ 
      191.84        14.40        14.70        11.70        11.87        15.29 
TCGA-B5-A1N2 TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 
       12.79        96.30        78.81        62.14        14.27        29.65 
TCGA-B5-A5OC TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       41.06        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-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 
       20.02        23.70        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-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-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-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-A16S TCGA-D1-A16V 
       29.92        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q 
       28.01        28.08        26.37        10.22         1.51         1.78 
TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU 
       11.15        24.30         2.33        22.92         1.41        13.22 
TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ TCGA-D1-A1O0 TCGA-D1-A1O5 
        0.72        18.25        16.87        18.02         2.07        15.06 
TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.27         4.11        89.33        10.92        27.16 
TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO 
       16.31        39.29        36.62        24.30        35.38         9.37 
TCGA-DI-A2QU TCGA-DI-A2QY TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 
       31.10       110.10        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        27.32        16.04         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        61.74        61.55        66.90        46.26        57.60 
TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.52        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        17.88        22.26        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        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-A1GX TCGA-EY-A1H0 TCGA-EY-A210 TCGA-EY-A212 TCGA-EY-A215 
       12.43         6.48        19.33        12.59        10.19        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX 
       22.82        20.05        45.76        31.04        27.35        13.84 
TCGA-EY-A547 TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 
       17.92        14.14        19.89        16.96        40.01        39.88 
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-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       25.02        29.23        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3W0 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       14.04         2.43        13.28        18.21        23.24        15.45 
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        12.92 
TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 
       23.64        14.83         4.44        14.07        18.28         0.07 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE 
                        0.20                         0.07 
  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 
                       23.97                        23.31 
[1] "0.2 - 116.2 (24.0)" "0.1 - 191.8 (23.3)"
[1] "hr=" "1.7"
D96V2, continuous
                              vv
clus                           ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 45(19P12) MUTATED                                        20
  DEL PEAK 45(19P12) WILD-TYPE                                     375
                              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                                  32
  DEL PEAK 45(19P12) WILD-TYPE                                80
D96V3, multiclass
                                         clus
vv                                        DEL PEAK 45(19P12) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                         20
  MIXED SEROUS AND ENDOMETRIOID                                    5
  SEROUS ENDOMETRIAL ADENOCARCINOMA                               32
                                         clus
vv                                        DEL PEAK 45(19P12) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          375
  MIXED SEROUS AND ENDOMETRIOID                                     16
  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"
D96V4, binary
                              cls
clus                             0   1
  DEL PEAK 45(19P12) MUTATED     8  49
  DEL PEAK 45(19P12) WILD-TYPE 133 338
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19P12) MUTATED      8   49
  DEL PEAK 45(19P12) WILD-TYPE  133  338
     clus
vv    DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE
  NO                           8                          133
  YES                         49                          338
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 45(19P12) MUTATED    33   3   2   7
  DEL PEAK 45(19P12) WILD-TYPE 330  20  15  28
D96V5, multiclass
    clus
vv   DEL PEAK 45(19P12) MUTATED DEL PEAK 45(19P12) WILD-TYPE
  R0                         33                          330
  R1                          3                           20
  R2                          2                           15
  RX                          7                           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 45(19P12) MUTATED                                  1     1
  DEL PEAK 45(19P12) WILD-TYPE                                3    19
                              vv
clus                           BLACK OR AFRICAN AMERICAN
  DEL PEAK 45(19P12) MUTATED                          17
  DEL PEAK 45(19P12) WILD-TYPE                        84
                              vv
clus                           NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 45(19P12) MUTATED                                           1    34
  DEL PEAK 45(19P12) WILD-TYPE                                         8   332
D96V6, multiclass
                                           clus
vv                                          DEL PEAK 45(19P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                   1
  ASIAN                                                              1
  BLACK OR AFRICAN AMERICAN                                         17
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                          1
  WHITE                                                             34
                                           clus
vv                                          DEL PEAK 45(19P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                     3
  ASIAN                                                               19
  BLACK OR AFRICAN AMERICAN                                           84
  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"
D96V7, binary
                              cls
clus                             0   1
  DEL PEAK 45(19P12) MUTATED     2  40
  DEL PEAK 45(19P12) WILD-TYPE  12 327
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 45(19P12) MUTATED      2   40
  DEL PEAK 45(19P12) WILD-TYPE   12  327
                        clus
vv                       DEL PEAK 45(19P12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         40
                        clus
vv                       DEL PEAK 45(19P12) WILD-TYPE
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          327
[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    48  16
  DEL PEAK 46(19Q13.43) WILD-TYPE 409  53
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             64                             462 
  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                             16                              53 
$`DEL PEAK 46(19Q13.43) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-A5-A2K2 
       41.06        36.69        65.75        60.53        19.96        91.04 
TCGA-A5-A2K4 TCGA-A5-A3LO TCGA-AJ-A23M TCGA-AJ-A23N TCGA-AJ-A3BI TCGA-AJ-A3IA 
       28.64         7.33         1.18        14.43        18.90        20.81 
TCGA-AJ-A3NF TCGA-AJ-A6NU TCGA-AP-A052 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H 
       21.21        20.78        21.99        63.91        57.80        45.53 
TCGA-AP-A0L8 TCGA-AP-A0L9 TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AX-A0IW TCGA-AX-A1C8 
       48.79       125.42        36.36        21.90        37.78        13.55 
TCGA-AX-A1CF TCGA-AX-A1CP TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H5 TCGA-AX-A2HK 
       76.83        36.39        11.08         4.77        71.24         2.96 
TCGA-AX-A3FZ TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-B5-A11P 
        0.20         1.38         0.30         0.26         0.30        36.82 
TCGA-B5-A1MS TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A5OE TCGA-BG-A18C TCGA-BG-A3PP 
      102.31        50.89        11.87        34.95        15.45         6.81 
TCGA-BK-A0CC TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A3DG TCGA-EO-A3KU TCGA-EY-A1GJ 
       10.22        27.42        11.51         4.27        22.26        23.90 
TCGA-EY-A1GW TCGA-EY-A210 TCGA-EY-A214 TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       11.08        12.59        14.40        29.10        27.35        13.84 
TCGA-FI-A2CY TCGA-FI-A2EW TCGA-FI-A2EX TCGA-FI-A2F8 TCGA-KJ-A3U4 TCGA-KP-A3VZ 
       41.06        59.01         9.07        25.02         2.43        23.74 
TCGA-KP-A3W3 TCGA-PG-A7D5 TCGA-QS-A8F1 TCGA-SL-A6J9 
       26.10        23.97         4.44         0.07 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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        10.26 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BD 
        0.39        19.79        29.39         2.40        34.36        34.16 
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        17.06        36.99        20.65        15.62        10.19 
TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AJ-A5DV 
       15.35        15.95        14.76        16.87        16.87        22.32 
TCGA-AJ-A5DW TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A053 TCGA-AP-A054 
       12.82         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        23.87        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-A1DQ TCGA-AP-A1DR TCGA-AP-A1DV TCGA-AP-A1E0 
       31.30        35.54        46.78        49.15         6.71        30.90 
TCGA-AP-A1E1 TCGA-AP-A1E3 TCGA-AP-A1E4 TCGA-AP-A5FX TCGA-AW-A1PO TCGA-AX-A05S 
       10.42        27.85        16.24        36.13         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-A1CA TCGA-AX-A1CC TCGA-AX-A1CE TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK 
       20.28        12.43        20.05        72.56        54.12        67.50 
TCGA-AX-A1CN TCGA-AX-A2H4 TCGA-AX-A2H7 TCGA-AX-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC 
       25.12        30.12        40.80        61.18        81.37        34.32 
TCGA-AX-A2HD TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2IN 
       46.49        19.36        26.33        17.75        30.74        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 
       64.93         0.23         0.20         0.56        43.82        20.52 
TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR 
        1.18        18.35        14.47         0.39        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        27.29        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-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-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-A3FH TCGA-B5-A3S1 
       96.30        78.81        62.14        33.11        14.27        29.65 
TCGA-B5-A5OC TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 
       41.06        34.13        18.61        20.19        19.33        20.94 
TCGA-BG-A0M3 TCGA-BG-A0M4 TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M8 TCGA-BG-A0M9 
       35.21        34.98        22.06        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        20.02        23.70        20.12 
TCGA-BG-A3EW TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B 
       11.31        35.90        34.98         6.21        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-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-A16J TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q 
       37.51        36.79        29.92        31.07        33.63        10.65 
TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 
        0.69        18.67         3.95         3.65        17.49        19.53 
TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B 
        6.64        30.15        18.02        14.73         1.58         7.00 
TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L 
        0.99        30.44         1.28        28.01        28.08        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NU TCGA-D1-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-A2G7 TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP 
       41.42         8.48        44.88         0.26         4.11        16.93 
TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY 
       89.33        10.92        27.16        16.31        39.29        36.62 
TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-DI-A2QY 
       24.30        35.38         9.37        12.39        31.10       110.10 
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        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW TCGA-EO-A3KX TCGA-EO-A3L0 
       27.16        17.88        26.96        16.34        14.53        24.89 
TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF 
        6.21        14.99         4.54        53.88        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-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-A212 TCGA-EY-A215 TCGA-EY-A2OM 
       15.81         6.48        19.33        10.19        18.87        22.82 
TCGA-EY-A2ON TCGA-EY-A2OO TCGA-EY-A2OP TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A548 
       20.05        45.76        31.04        11.38        17.92        14.14 
TCGA-EY-A549 TCGA-EY-A54A TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2D0 
       19.89        14.70        16.96         5.88        40.01        39.88 
TCGA-FI-A2D2 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EU TCGA-FI-A2EY 
       39.95         7.99        13.84         8.98        96.69        28.93 
TCGA-FI-A2F4 TCGA-FI-A2F9 TCGA-FI-A3PV TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.96        29.23        41.06        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB 
       14.04        13.28         9.47        18.21        23.24        15.45 
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 TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6JA 
       12.92        23.64        14.83        14.07        18.28         0.23 

  DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE 
                           0.07                            0.13 
  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 
                         21.945                          23.425 
[1] "0.1 - 125.4 (21.9)" "0.1 - 191.8 (23.4)"
[1] "hr=" "2.4"
D97V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 46(19Q13.43) MUTATED                                        19
  DEL PEAK 46(19Q13.43) WILD-TYPE                                     376
                                 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                                  42
  DEL PEAK 46(19Q13.43) WILD-TYPE                                70
D97V3, multiclass
                                         clus
vv                                        DEL PEAK 46(19Q13.43) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            19
  MIXED SEROUS AND ENDOMETRIOID                                       4
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  42
                                         clus
vv                                        DEL PEAK 46(19Q13.43) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             376
  MIXED SEROUS AND ENDOMETRIOID                                        17
  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"
D97V4, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.43) MUTATED    14  51
  DEL PEAK 46(19Q13.43) WILD-TYPE 127 336
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.43) MUTATED     14   51
  DEL PEAK 46(19Q13.43) WILD-TYPE  127  336
     clus
vv    DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE
  NO                             14                             127
  YES                            51                             336
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(19Q13.43) MUTATED    36   6   3   7
  DEL PEAK 46(19Q13.43) WILD-TYPE 327  17  14  28
D97V5, multiclass
    clus
vv   DEL PEAK 46(19Q13.43) MUTATED DEL PEAK 46(19Q13.43) WILD-TYPE
  R0                            36                             327
  R1                             6                              17
  R2                             3                              14
  RX                             7                              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 46(19Q13.43) MUTATED                                  0     0
  DEL PEAK 46(19Q13.43) WILD-TYPE                                4    20
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 46(19Q13.43) MUTATED                          18
  DEL PEAK 46(19Q13.43) WILD-TYPE                        83
                                 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      44
  DEL PEAK 46(19Q13.43) WILD-TYPE   322
D97V6, multiclass
                                           clus
vv                                          DEL PEAK 46(19Q13.43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      0
  ASIAN                                                                 0
  BLACK OR AFRICAN AMERICAN                                            18
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             1
  WHITE                                                                44
                                           clus
vv                                          DEL PEAK 46(19Q13.43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        4
  ASIAN                                                                  20
  BLACK OR AFRICAN AMERICAN                                              83
  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"
D97V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(19Q13.43) MUTATED     3  43
  DEL PEAK 46(19Q13.43) WILD-TYPE  11 324
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(19Q13.43) MUTATED      3   43
  DEL PEAK 46(19Q13.43) WILD-TYPE   11  324
                        clus
vv                       DEL PEAK 46(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            43
                        clus
vv                       DEL PEAK 46(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                  11
  NOT HISPANIC OR LATINO                             324
[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    22  13
  DEL PEAK 47(20P12.1) WILD-TYPE 435  56
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            35                            491 
  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                            13                             56 
$`DEL PEAK 47(20P12.1) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0G2 TCGA-A5-A0GN TCGA-A5-A0R6 TCGA-AJ-A23M TCGA-AJ-A3BD 
       41.06       149.56        60.53        19.96         1.18        34.16 
TCGA-AP-A05H TCGA-AP-A0LH TCGA-AP-A3K1 TCGA-AX-A1CF TCGA-AX-A2H2 TCGA-AX-A2H7 
       45.53        36.36        21.90        76.83         4.77        40.80 
TCGA-AX-A3G1 TCGA-AX-A3G4 TCGA-B5-A0K8 TCGA-B5-A1MS TCGA-B5-A3FH TCGA-B5-A5OE 
       20.52         0.30        17.85       102.31        14.27        34.95 
TCGA-BG-A0M6 TCGA-BG-A0MG TCGA-BG-A0MO TCGA-BG-A18C TCGA-BK-A4ZD TCGA-D1-A161 
       22.06        48.56        43.04        15.45        16.64        29.33 
TCGA-D1-A17M TCGA-D1-A3JP TCGA-DI-A1NO TCGA-DI-A2QT TCGA-EY-A1GW TCGA-EY-A2OQ 
       10.22        16.93         9.37        12.39        11.08        29.10 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-FI-A2D2 TCGA-FI-A3PV TCGA-QS-A8F1 
       11.38        17.92        39.95        41.06         4.44 

$`DEL PEAK 47(20P12.1) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G5 TCGA-A5-A0G9 TCGA-A5-A0GA 
       36.69        10.29       106.88        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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-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-A1OH 
       29.06        42.35        15.95         7.92        11.44        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-A23N TCGA-AJ-A23O TCGA-AJ-A2QK 
        5.16         7.33        14.96        14.43        10.26         0.39 
TCGA-AJ-A2QL TCGA-AJ-A2QM TCGA-AJ-A2QN TCGA-AJ-A2QO TCGA-AJ-A3BF TCGA-AJ-A3BG 
       19.79        29.39         2.40        34.36         1.12         0.76 
TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3EM 
       18.90         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 
       17.06        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A3QS TCGA-AJ-A3TW 
       10.19        15.35        15.95        14.76        16.87        16.87 
TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 
       22.32        12.82        20.78         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        63.91 
TCGA-AP-A05D TCGA-AP-A05J TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P TCGA-AP-A0L8 
       57.80        36.89        23.87        12.20        20.91        48.79 
TCGA-AP-A0L9 TCGA-AP-A0LD TCGA-AP-A0LE TCGA-AP-A0LF TCGA-AP-A0LG TCGA-AP-A0LI 
      125.42       117.99       110.37         3.39        63.16        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        46.78        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        36.13         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-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-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-A2H8 TCGA-AX-A2HA TCGA-AX-A2HC TCGA-AX-A2HD 
       30.12        71.24        61.18        81.37        34.32        46.49 
TCGA-AX-A2HF TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK TCGA-AX-A2IN 
       19.36        26.33        17.75        30.74         2.96        31.13 
TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3FZ 
       64.93         0.23         0.20         0.56        43.82         0.20 
TCGA-AX-A3G3 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 TCGA-AX-A3GB 
        1.38         0.26         0.30         1.18        18.35        14.47 
TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
        0.39        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-A0K3 TCGA-B5-A0K4 TCGA-B5-A0K6 TCGA-B5-A0K7 TCGA-B5-A0K9 
       25.91        27.29        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-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-A3S1 TCGA-B5-A5OC TCGA-B5-A5OD 
       78.81        62.14        33.11        29.65        41.06        34.13 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        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-A0MQ TCGA-BG-A0MS TCGA-BG-A0MT TCGA-BG-A0MU TCGA-BG-A0RY 
       43.30        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        20.02        23.70 
TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA TCGA-BK-A0CB 
       20.12        11.31         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-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-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-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-A163 TCGA-D1-A165 TCGA-D1-A167 TCGA-D1-A168 TCGA-D1-A169 
        3.68        32.58         0.66        15.72        36.10        37.32 
TCGA-D1-A16B TCGA-D1-A16D TCGA-D1-A16E TCGA-D1-A16G TCGA-D1-A16I TCGA-D1-A16J 
       36.36        37.51        36.79        27.42        11.51        29.92 
TCGA-D1-A16N TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16V 
       31.07        33.63        10.65         0.69        18.67         3.95 
TCGA-D1-A16X TCGA-D1-A16Y TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 
        3.65        17.49        19.53         6.64        30.15        18.02 
TCGA-D1-A179 TCGA-D1-A17A TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F 
       14.73         1.58         7.00         0.99        30.44         1.28 
TCGA-D1-A17H TCGA-D1-A17K TCGA-D1-A17L TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R 
       28.01        28.08        26.37         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-A3DG TCGA-D1-A3DH TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ TCGA-DI-A0WH 
        4.27         4.11        89.33        10.92        27.16        16.31 
TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN TCGA-DI-A2QU TCGA-DI-A2QY 
       39.29        36.62        24.30        35.38        31.10       110.10 
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        27.32 
TCGA-EC-A1NJ TCGA-EC-A1QX TCGA-EC-A24G TCGA-EO-A1Y5 TCGA-EO-A1Y7 TCGA-EO-A1Y8 
       16.04         7.36        16.80        10.92        49.15        37.71 
TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y 
       61.74        61.55        66.90        46.26        57.60        51.52 
TCGA-EO-A2CG TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY 
       51.42        19.40        34.39        26.43        35.15        17.19 
TCGA-EO-A3AZ TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KU TCGA-EO-A3KW TCGA-EO-A3KX 
       27.16        17.88        26.96        22.26        16.34        14.53 
TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD TCGA-EY-A1GE 
       24.89         6.21        14.99         4.54        53.88        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-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 
       10.19        14.40        18.87        22.82        20.05        45.76 
TCGA-EY-A2OP TCGA-EY-A3L3 TCGA-EY-A3QX TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       31.04        27.35        13.84        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY TCGA-FI-A2D0 TCGA-FI-A2D4 
       16.96         5.88        40.01        41.06        39.88         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-JU-AAVI 
       28.96        25.02        29.23        45.01         1.74         7.76 
TCGA-K6-A3WQ TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W0 TCGA-KP-A3W1 TCGA-KP-A3W3 
       14.04         2.43        23.74        13.28         9.47        26.10 
TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       18.21        23.24        15.45        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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE 
                          0.30                           0.07 
  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 
                         21.90                          23.38 
[1] "0.3 - 149.6 (21.9)" "0.1 - 191.8 (23.4)"
[1] "hr=" "3.2"
D98V2, continuous
                                vv
clus                             ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 47(20P12.1) MUTATED                                        16
  DEL PEAK 47(20P12.1) WILD-TYPE                                     379
                                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                                  17
  DEL PEAK 47(20P12.1) WILD-TYPE                                95
D98V3, multiclass
                                         clus
vv                                        DEL PEAK 47(20P12.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           16
  MIXED SEROUS AND ENDOMETRIOID                                      2
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                 17
                                         clus
vv                                        DEL PEAK 47(20P12.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            379
  MIXED SEROUS AND ENDOMETRIOID                                       19
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                   95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D98V4, binary
                                cls
clus                               0   1
  DEL PEAK 47(20P12.1) MUTATED     9  26
  DEL PEAK 47(20P12.1) WILD-TYPE 132 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      9   26
  DEL PEAK 47(20P12.1) WILD-TYPE  132  361
     clus
vv    DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  NO                             9                            132
  YES                           26                            361
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(20P12.1) MUTATED    20   1   2   5
  DEL PEAK 47(20P12.1) WILD-TYPE 343  22  15  30
D98V5, multiclass
    clus
vv   DEL PEAK 47(20P12.1) MUTATED DEL PEAK 47(20P12.1) WILD-TYPE
  R0                           20                            343
  R1                            1                             22
  R2                            2                             15
  RX                            5                             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
  DEL PEAK 47(20P12.1) MUTATED                                  1     1
  DEL PEAK 47(20P12.1) WILD-TYPE                                3    19
                                vv
clus                             BLACK OR AFRICAN AMERICAN
  DEL PEAK 47(20P12.1) MUTATED                          10
  DEL PEAK 47(20P12.1) WILD-TYPE                        91
                                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      21
  DEL PEAK 47(20P12.1) WILD-TYPE   345
D98V6, multiclass
                                           clus
vv                                          DEL PEAK 47(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                     1
  ASIAN                                                                1
  BLACK OR AFRICAN AMERICAN                                           10
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                            1
  WHITE                                                               21
                                           clus
vv                                          DEL PEAK 47(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                       3
  ASIAN                                                                 19
  BLACK OR AFRICAN AMERICAN                                             91
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                              8
  WHITE                                                                345
[1] 5 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  27
  DEL PEAK 47(20P12.1) WILD-TYPE  12 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(20P12.1) MUTATED      2   27
  DEL PEAK 47(20P12.1) WILD-TYPE   12  340
                        clus
vv                       DEL PEAK 47(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       DEL PEAK 47(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            340
[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   107  28
  DEL PEAK 48(22Q13.32) WILD-TYPE 350  41
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            135                             391 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                             28                              41 
$`DEL PEAK 48(22Q13.32) MUTATED`
TCGA-2E-A9G8 TCGA-A5-A0GJ TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R6 TCGA-A5-A0R7 
       41.06        65.75        60.53        36.82        19.96        17.59 
TCGA-A5-A1OH TCGA-A5-A2K2 TCGA-A5-A3LO TCGA-A5-A3LP TCGA-AJ-A23M TCGA-AJ-A23N 
       36.33        91.04         7.33        14.96         1.18        14.43 
TCGA-AJ-A2QK TCGA-AJ-A2QL TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3BI TCGA-AJ-A3EJ 
        0.39        19.79        34.16         1.12        18.90         1.64 
TCGA-AJ-A3EM TCGA-AJ-A3I9 TCGA-AJ-A3IA TCGA-AJ-A3NH TCGA-AJ-A3TW TCGA-AP-A052 
       22.26        17.06        20.81        10.19        16.87        21.99 
TCGA-AP-A053 TCGA-AP-A05A TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A0L8 TCGA-AP-A0LF 
        5.95        63.91        57.80        45.53        48.79         3.39 
TCGA-AP-A0LI TCGA-AP-A1DQ TCGA-AP-A5FX TCGA-AX-A06B TCGA-AX-A0IU TCGA-AX-A0IW 
       97.71        46.78        36.13        53.92        28.54        37.78 
TCGA-AX-A1C7 TCGA-AX-A1C8 TCGA-AX-A1CA TCGA-AX-A1CP TCGA-AX-A2H2 TCGA-AX-A2H4 
       16.96        13.55        20.28        36.39         4.77        30.12 
TCGA-AX-A2H5 TCGA-AX-A2H8 TCGA-AX-A2HC TCGA-AX-A2HF TCGA-AX-A2HK TCGA-AX-A2IO 
       71.24        61.18        34.32        19.36         2.96        64.93 
TCGA-AX-A3FW TCGA-AX-A3FX TCGA-AX-A3G1 TCGA-AX-A3G3 TCGA-AX-A3G4 TCGA-AX-A3G6 
        0.56        43.82        20.52         1.38         0.30         0.26 
TCGA-AX-A3G7 TCGA-B5-A0K8 TCGA-B5-A0KB TCGA-B5-A11I TCGA-B5-A11P TCGA-B5-A1MS 
        0.30        17.85         4.11        75.72        36.82       102.31 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3F9 TCGA-B5-A3FD TCGA-B5-A5OD 
       50.89        11.87        12.79       116.25        33.11        34.13 
TCGA-BG-A0M8 TCGA-BG-A0MT TCGA-BG-A0VZ TCGA-BG-A0YV TCGA-BG-A18C TCGA-BG-A2AD 
       36.49        21.17        52.64        12.56        15.45        20.02 
TCGA-BG-A3PP TCGA-BK-A0CA TCGA-BK-A0CC TCGA-BK-A139 TCGA-BS-A0U9 TCGA-D1-A0ZP 
        6.81        34.98        10.22        10.16        67.20        29.95 
TCGA-D1-A0ZQ TCGA-D1-A0ZZ TCGA-D1-A15X TCGA-D1-A16I TCGA-D1-A16N TCGA-D1-A16S 
        8.55        22.55        29.88        11.51        31.07        18.67 
TCGA-D1-A16V TCGA-D1-A179 TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1NW TCGA-D1-A1NX 
        3.95        14.73        28.08        13.22         0.72        18.25 
TCGA-D1-A3DG TCGA-DI-A1NN TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QU TCGA-E6-A2P9 
        4.27        35.38         9.37        12.39        31.10         6.67 
TCGA-E6-A8L9 TCGA-EO-A1Y7 TCGA-EO-A2CG TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EO-A3KW 
       27.32        49.15        51.42        27.16        22.26        16.34 
TCGA-EY-A1GC TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GR TCGA-EY-A1GW TCGA-EY-A210 
        4.54        23.90        18.84        17.62        11.08        12.59 
TCGA-EY-A212 TCGA-EY-A214 TCGA-EY-A2OO TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A3QX 
       10.19        14.40        45.76        29.10        27.35        13.84 
TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A72D TCGA-FI-A2CY TCGA-FI-A2D2 TCGA-FI-A2EU 
       11.38        17.92         5.88        41.06        39.95        96.69 
TCGA-FI-A2EX TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI TCGA-K6-A3WQ 
        9.07        29.23        45.01         1.74         7.76        14.04 
TCGA-KJ-A3U4 TCGA-KP-A3VZ TCGA-KP-A3W3 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-PG-A7D5 
        2.43        23.74        26.10        18.21        23.24        23.97 
TCGA-PG-A914 TCGA-PG-A915 TCGA-SL-A6J9 
       12.92         7.00         0.07 

$`DEL PEAK 48(22Q13.32) WILD-TYPE`
TCGA-5B-A90C TCGA-5S-A9Q8 TCGA-A5-A0G1 TCGA-A5-A0G2 TCGA-A5-A0G5 TCGA-A5-A0G9 
       36.69        10.29       106.88       149.56        37.02        83.51 
TCGA-A5-A0GA TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH 
       17.85        32.78       112.54       105.37        87.32        74.10 
TCGA-A5-A0GI TCGA-A5-A0GM TCGA-A5-A0GP TCGA-A5-A0GQ TCGA-A5-A0GU TCGA-A5-A0GV 
       57.53        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-A0VP 
       23.21        68.65        19.59        24.62        29.06        42.35 
TCGA-A5-A0VQ TCGA-A5-A1OF TCGA-A5-A1OG TCGA-A5-A1OJ TCGA-A5-A1OK TCGA-A5-A2K3 
       15.95         7.92        11.44         9.60         8.02        46.32 
TCGA-A5-A2K4 TCGA-A5-A2K5 TCGA-A5-A2K7 TCGA-AJ-A23O TCGA-AJ-A2QM TCGA-AJ-A2QN 
       28.64         5.33         5.16        10.26        29.39         2.40 
TCGA-AJ-A2QO TCGA-AJ-A3BG TCGA-AJ-A3BK TCGA-AJ-A3EK TCGA-AJ-A3EL TCGA-AJ-A3NC 
       34.36         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        21.21        15.62        15.35        15.95        14.76 
TCGA-AJ-A3QS TCGA-AJ-A5DV TCGA-AJ-A5DW TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW 
       16.87        22.32        12.82        20.78         2.70         0.13 
TCGA-AP-A051 TCGA-AP-A054 TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05J TCGA-AP-A05N 
       83.67        23.31        86.07         8.22        36.89        23.87 
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-AW-A1PO 
       30.90        10.42        27.85        16.24        21.90         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-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-A0IZ TCGA-AX-A0J0 
       27.39        30.02        60.66        35.01        43.82        40.11 
TCGA-AX-A0J1 TCGA-AX-A1C4 TCGA-AX-A1C5 TCGA-AX-A1C9 TCGA-AX-A1CC TCGA-AX-A1CE 
       65.88        13.28        19.20        15.25        12.43        20.05 
TCGA-AX-A1CF TCGA-AX-A1CI TCGA-AX-A1CJ TCGA-AX-A1CK TCGA-AX-A1CN TCGA-AX-A1CR 
       76.83        72.56        54.12        67.50        25.12        11.08 
TCGA-AX-A2H7 TCGA-AX-A2HA TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ 
       40.80        81.37        46.49        26.33        17.75        30.74 
TCGA-AX-A2IN TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FZ TCGA-AX-A3G8 TCGA-AX-A3G9 
       31.13         0.23         0.20         0.20         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JN TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT 
       14.47         0.39        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        27.29        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-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC TCGA-B5-A5OE 
       78.81        62.14        14.27        29.65        41.06        34.95 
TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 TCGA-BG-A0M4 
       18.61        20.19        19.33        20.94        35.21        34.98 
TCGA-BG-A0M6 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       22.06        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-A0W1 
       15.42        24.39        26.66        16.34        34.29        52.83 
TCGA-BG-A0W2 TCGA-BG-A0YU TCGA-BG-A186 TCGA-BG-A187 TCGA-BG-A18A TCGA-BG-A18B 
       56.58        14.83        13.78        14.73        14.01        15.45 
TCGA-BG-A220 TCGA-BG-A221 TCGA-BG-A222 TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW 
       14.27         1.81         9.57        23.70        20.12        11.31 
TCGA-BK-A0C9 TCGA-BK-A0CB TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A4ZD 
       35.90         6.21        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-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-A0ZR TCGA-D1-A0ZS 
       63.16        66.48        16.83        19.79         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-A15Z TCGA-D1-A160 TCGA-D1-A161 TCGA-D1-A163 TCGA-D1-A165 
       30.08         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-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16X 
       27.42        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-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-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-A2G7 
        1.05         3.95         3.52        41.42         8.48        44.88 
TCGA-D1-A3DA TCGA-D1-A3DH TCGA-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY TCGA-DF-A2KZ 
        0.26         4.11        16.93        89.33        10.92        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       110.10        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        16.04         7.36        16.80 
TCGA-EO-A1Y5 TCGA-EO-A1Y8 TCGA-EO-A22R TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U 
       10.92        37.71        61.74        61.55        66.90        46.26 
TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A2CH TCGA-EO-A3AS TCGA-EO-A3AU TCGA-EO-A3AV 
       57.60        51.52        19.40        34.39        26.43        35.15 
TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 
       17.19        17.88        26.96        14.53        24.89         6.21 
TCGA-EY-A1G8 TCGA-EY-A1GD TCGA-EY-A1GE TCGA-EY-A1GF TCGA-EY-A1GH TCGA-EY-A1GI 
       14.99        53.88        24.36        27.16        23.34        23.34 
TCGA-EY-A1GK TCGA-EY-A1GL TCGA-EY-A1GM TCGA-EY-A1GO TCGA-EY-A1GQ TCGA-EY-A1GS 
       22.78        13.97         6.90        19.27        17.88        15.09 
TCGA-EY-A1GT TCGA-EY-A1GU TCGA-EY-A1GV TCGA-EY-A1GX TCGA-EY-A1H0 TCGA-EY-A215 
       16.11        12.43        15.81         6.48        19.33        18.87 
TCGA-EY-A2OM TCGA-EY-A2ON TCGA-EY-A2OP TCGA-EY-A548 TCGA-EY-A549 TCGA-EY-A54A 
       22.82        20.05        31.04        14.14        19.89        14.70 
TCGA-EY-A5W2 TCGA-FI-A2CX TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 
       16.96        40.01        39.88         7.99        13.84         8.98 
TCGA-FI-A2EW TCGA-FI-A2EY TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A3PV TCGA-KP-A3W0 
       59.01        28.93        28.96        25.02        41.06        13.28 
TCGA-KP-A3W1 TCGA-PG-A6IB TCGA-PG-A916 TCGA-PG-A917 TCGA-QF-A5YS TCGA-QF-A5YT 
        9.47        15.45        11.24         6.97        18.84        39.95 
TCGA-QS-A5YQ TCGA-QS-A5YR TCGA-QS-A744 TCGA-QS-A8F1 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ 
       12.92        23.64        14.83         4.44        14.07        18.28 
TCGA-SL-A6JA 
        0.23 

  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                           0.07                            0.13 
  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 
                          19.96                           24.30 
[1] "0.1 - 116.2 (20.0)" "0.1 - 191.8 (24.3)"
[1] "hr=" "2.4"
D99V2, continuous
                                 vv
clus                              ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                                        54
  DEL PEAK 48(22Q13.32) WILD-TYPE                                     341
                                 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                                  72
  DEL PEAK 48(22Q13.32) WILD-TYPE                                40
D99V3, multiclass
                                         clus
vv                                        DEL PEAK 48(22Q13.32) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                            54
  MIXED SEROUS AND ENDOMETRIOID                                      10
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                  72
                                         clus
vv                                        DEL PEAK 48(22Q13.32) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                             341
  MIXED SEROUS AND ENDOMETRIOID                                        11
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                    40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D99V4, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED    26 110
  DEL PEAK 48(22Q13.32) WILD-TYPE 115 277
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED     26  110
  DEL PEAK 48(22Q13.32) WILD-TYPE  115  277
     clus
vv    DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  NO                             26                             115
  YES                           110                             277
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(22Q13.32) MUTATED    88   6   6  13
  DEL PEAK 48(22Q13.32) WILD-TYPE 275  17  11  22
D99V5, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  R0                            88                             275
  R1                             6                              17
  R2                             6                              11
  RX                            13                              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 48(22Q13.32) MUTATED                                  1     1
  DEL PEAK 48(22Q13.32) WILD-TYPE                                3    19
                                 vv
clus                              BLACK OR AFRICAN AMERICAN
  DEL PEAK 48(22Q13.32) MUTATED                          37
  DEL PEAK 48(22Q13.32) WILD-TYPE                        64
                                 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      89
  DEL PEAK 48(22Q13.32) WILD-TYPE   277
D99V6, multiclass
                                           clus
vv                                          DEL PEAK 48(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                      1
  ASIAN                                                                 1
  BLACK OR AFRICAN AMERICAN                                            37
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             2
  WHITE                                                                89
                                           clus
vv                                          DEL PEAK 48(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                        3
  ASIAN                                                                  19
  BLACK OR AFRICAN AMERICAN                                              64
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                               7
  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"
D99V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED     6  99
  DEL PEAK 48(22Q13.32) WILD-TYPE   8 268
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED      6   99
  DEL PEAK 48(22Q13.32) WILD-TYPE    8  268
                        clus
vv                       DEL PEAK 48(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            99
                        clus
vv                       DEL PEAK 48(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             268
[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    60  23
  DEL PEAK 49(XP21.1) WILD-TYPE 397  46
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           83                           443 
  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                           23                            46 
$`DEL PEAK 49(XP21.1) MUTATED`
TCGA-2E-A9G8 TCGA-5B-A90C TCGA-A5-A0GN TCGA-A5-A0GR TCGA-A5-A0R7 TCGA-A5-A1OH 
       41.06        36.69        60.53        36.82        17.59        36.33 
TCGA-A5-A2K2 TCGA-A5-A3LP TCGA-AJ-A23N TCGA-AJ-A3BD TCGA-AJ-A3BF TCGA-AJ-A3I9 
       91.04        14.96        14.43        34.16         1.12        17.06 
TCGA-AJ-A3QS TCGA-AJ-A3TW TCGA-AP-A053 TCGA-AP-A05D TCGA-AP-A05H TCGA-AP-A05J 
       16.87        16.87         5.95        57.80        45.53        36.89 
TCGA-AP-A0L8 TCGA-AP-A0LI TCGA-AW-A1PO TCGA-AX-A06B TCGA-AX-A1C7 TCGA-AX-A1CK 
       48.79        97.71         0.56        53.92        16.96        67.50 
TCGA-AX-A1CR TCGA-AX-A2H2 TCGA-AX-A2H4 TCGA-AX-A2H8 TCGA-AX-A2HF TCGA-AX-A3G3 
       11.08         4.77        30.12        61.18        19.36         1.38 
TCGA-AX-A3G4 TCGA-B5-A0JN TCGA-B5-A0K3 TCGA-B5-A0K8 TCGA-B5-A11G TCGA-B5-A11P 
        0.30        80.38        27.29        17.85       113.36        36.82 
TCGA-B5-A1MU TCGA-B5-A1MY TCGA-B5-A1N2 TCGA-B5-A3FD TCGA-B5-A5OE TCGA-BG-A0M6 
       50.89        11.87        12.79        33.11        34.95        22.06 
TCGA-BG-A0M8 TCGA-BG-A0YV TCGA-BG-A18C TCGA-BK-A0CC TCGA-BK-A4ZD TCGA-D1-A16I 
       36.49        12.56        15.45        10.22        16.64        11.51 
TCGA-D1-A16N TCGA-D1-A16V TCGA-D1-A17K TCGA-D1-A1NU TCGA-D1-A1O0 TCGA-D1-A3DG 
       31.07         3.95        28.08        13.22         2.07         4.27 
TCGA-DI-A1NO TCGA-DI-A2QT TCGA-DI-A2QY TCGA-E6-A8L9 TCGA-EO-A1Y5 TCGA-EO-A2CG 
        9.37        12.39       110.10        27.32        10.92        51.42 
TCGA-EO-A2CH TCGA-EO-A3AZ TCGA-EO-A3KU TCGA-EY-A1GJ TCGA-EY-A1GP TCGA-EY-A1GW 
       19.40        27.16        22.26        23.90        18.84        11.08 
TCGA-EY-A2ON TCGA-EY-A2OQ TCGA-EY-A3L3 TCGA-EY-A4KR TCGA-EY-A547 TCGA-EY-A54A 
       20.05        29.10        27.35        11.38        17.92        14.70 
TCGA-FI-A2D2 TCGA-FI-A2EU TCGA-FI-A2EY TCGA-FI-A3PV TCGA-K6-A3WQ TCGA-KJ-A3U4 
       39.95        96.69        28.93        41.06        14.04         2.43 
TCGA-KP-A3VZ TCGA-KP-A3W1 TCGA-KP-A3W4 TCGA-PG-A5BC TCGA-QS-A8F1 
       23.74         9.47        18.21        23.24         4.44 

$`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 
       10.29       106.88       149.56        37.02        83.51        17.85 
TCGA-A5-A0GB TCGA-A5-A0GD TCGA-A5-A0GE TCGA-A5-A0GG TCGA-A5-A0GH TCGA-A5-A0GI 
       32.78       112.54       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 
       10.26         0.39        19.79        29.39         2.40        34.36 
TCGA-AJ-A3BG TCGA-AJ-A3BI TCGA-AJ-A3BK TCGA-AJ-A3EJ TCGA-AJ-A3EK TCGA-AJ-A3EL 
        0.76        18.90         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        20.81        36.99        20.65        21.21        15.62 
TCGA-AJ-A3NH TCGA-AJ-A3OJ TCGA-AJ-A3OK TCGA-AJ-A3OL TCGA-AJ-A5DV TCGA-AJ-A5DW 
       10.19        15.35        15.95        14.76        22.32        12.82 
TCGA-AJ-A6NU TCGA-AJ-A8CT TCGA-AJ-A8CW TCGA-AP-A051 TCGA-AP-A052 TCGA-AP-A054 
       20.78         2.70         0.13        83.67        21.99        23.31 
TCGA-AP-A056 TCGA-AP-A059 TCGA-AP-A05A TCGA-AP-A05N TCGA-AP-A05O TCGA-AP-A05P 
       86.07         8.22        63.91        23.87        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-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        46.78        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        21.90        36.13 
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-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-A2H7 TCGA-AX-A2HA 
       54.12        25.12        36.39        71.24        40.80        81.37 
TCGA-AX-A2HC TCGA-AX-A2HD TCGA-AX-A2HG TCGA-AX-A2HH TCGA-AX-A2HJ TCGA-AX-A2HK 
       34.32        46.49        26.33        17.75        30.74         2.96 
TCGA-AX-A2IN TCGA-AX-A2IO TCGA-AX-A3FS TCGA-AX-A3FT TCGA-AX-A3FW TCGA-AX-A3FX 
       31.13        64.93         0.23         0.20         0.56        43.82 
TCGA-AX-A3FZ TCGA-AX-A3G1 TCGA-AX-A3G6 TCGA-AX-A3G7 TCGA-AX-A3G8 TCGA-AX-A3G9 
        0.20        20.52         0.26         0.30         1.18        18.35 
TCGA-AX-A3GB TCGA-AX-A3GI TCGA-B5-A0JR TCGA-B5-A0JS TCGA-B5-A0JT TCGA-B5-A0JU 
       14.47         0.39        56.91        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-A11H TCGA-B5-A11I TCGA-B5-A11J TCGA-B5-A11L 
        8.71       185.79        88.34        75.72        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-A1MS TCGA-B5-A1MV TCGA-B5-A1MW TCGA-B5-A1MX TCGA-B5-A1MZ TCGA-B5-A3F9 
      102.31        14.40        14.70        11.70        15.29       116.25 
TCGA-B5-A3FA TCGA-B5-A3FB TCGA-B5-A3FC TCGA-B5-A3FH TCGA-B5-A3S1 TCGA-B5-A5OC 
       96.30        78.81        62.14        14.27        29.65        41.06 
TCGA-B5-A5OD TCGA-BG-A0LW TCGA-BG-A0LX TCGA-BG-A0M0 TCGA-BG-A0M2 TCGA-BG-A0M3 
       34.13        18.61        20.19        19.33        20.94        35.21 
TCGA-BG-A0M4 TCGA-BG-A0M7 TCGA-BG-A0M9 TCGA-BG-A0MA TCGA-BG-A0MC TCGA-BG-A0MG 
       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-A221 TCGA-BG-A222 TCGA-BG-A2AD 
       14.01        15.45        14.27         1.81         9.57        20.02 
TCGA-BG-A2AE TCGA-BG-A2L7 TCGA-BG-A3EW TCGA-BG-A3PP TCGA-BK-A0C9 TCGA-BK-A0CA 
       23.70        20.12        11.31         6.81        35.90        34.98 
TCGA-BK-A0CB TCGA-BK-A139 TCGA-BK-A13B TCGA-BK-A13C TCGA-BK-A26L TCGA-BK-A56F 
        6.21        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-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-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-A16J 
       37.32        36.36        37.51        36.79        27.42        29.92 
TCGA-D1-A16O TCGA-D1-A16Q TCGA-D1-A16R TCGA-D1-A16S TCGA-D1-A16X TCGA-D1-A16Y 
       33.63        10.65         0.69        18.67         3.65        17.49 
TCGA-D1-A174 TCGA-D1-A175 TCGA-D1-A176 TCGA-D1-A177 TCGA-D1-A179 TCGA-D1-A17A 
       19.53         6.64        30.15        18.02        14.73         1.58 
TCGA-D1-A17B TCGA-D1-A17C TCGA-D1-A17D TCGA-D1-A17F TCGA-D1-A17H TCGA-D1-A17L 
        7.00         0.99        30.44         1.28        28.01        26.37 
TCGA-D1-A17M TCGA-D1-A17N TCGA-D1-A17Q TCGA-D1-A17R TCGA-D1-A17S TCGA-D1-A17T 
       10.22         1.51         1.78        11.15        24.30         2.33 
TCGA-D1-A17U TCGA-D1-A1NS TCGA-D1-A1NW TCGA-D1-A1NX TCGA-D1-A1NY TCGA-D1-A1NZ 
       22.92         1.41         0.72        18.25        16.87        18.02 
TCGA-D1-A1O5 TCGA-D1-A1O7 TCGA-D1-A1O8 TCGA-D1-A2G0 TCGA-D1-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-D1-A3JP TCGA-DF-A2KV TCGA-DF-A2KY 
       44.88         0.26         4.11        16.93        89.33        10.92 
TCGA-DF-A2KZ TCGA-DI-A0WH TCGA-DI-A1BU TCGA-DI-A1BY TCGA-DI-A1C3 TCGA-DI-A1NN 
       27.16        16.31        39.29        36.62        24.30        35.38 
TCGA-DI-A2QU TCGA-E6-A1LX TCGA-E6-A1LZ TCGA-E6-A1M0 TCGA-E6-A2P8 TCGA-E6-A2P9 
       31.10        23.38        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 
       16.04         7.36        16.80        49.15        37.71        61.74 
TCGA-EO-A22S TCGA-EO-A22T TCGA-EO-A22U TCGA-EO-A22X TCGA-EO-A22Y TCGA-EO-A3AS 
       61.55        66.90        46.26        57.60        51.52        34.39 
TCGA-EO-A3AU TCGA-EO-A3AV TCGA-EO-A3AY TCGA-EO-A3B0 TCGA-EO-A3B1 TCGA-EO-A3KW 
       26.43        35.15        17.19        17.88        26.96        16.34 
TCGA-EO-A3KX TCGA-EO-A3L0 TCGA-EY-A1G7 TCGA-EY-A1G8 TCGA-EY-A1GC TCGA-EY-A1GD 
       14.53        24.89         6.21        14.99         4.54        53.88 
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-A1GQ TCGA-EY-A1GR TCGA-EY-A1GS TCGA-EY-A1GT 
        6.90        19.27        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-A212 
       12.43        15.81         6.48        19.33        12.59        10.19 
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-A548 TCGA-EY-A549 TCGA-EY-A5W2 TCGA-EY-A72D TCGA-FI-A2CX TCGA-FI-A2CY 
       14.14        19.89        16.96         5.88        40.01        41.06 
TCGA-FI-A2D0 TCGA-FI-A2D4 TCGA-FI-A2D5 TCGA-FI-A2D6 TCGA-FI-A2EW TCGA-FI-A2EX 
       39.88         7.99        13.84         8.98        59.01         9.07 
TCGA-FI-A2F4 TCGA-FI-A2F8 TCGA-FI-A2F9 TCGA-FI-A3PX TCGA-H5-A2HR TCGA-JU-AAVI 
       28.96        25.02        29.23        45.01         1.74         7.76 
TCGA-KP-A3W0 TCGA-KP-A3W3 TCGA-PG-A6IB TCGA-PG-A7D5 TCGA-PG-A914 TCGA-PG-A915 
       13.28        26.10        15.45        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        12.92        23.64 
TCGA-QS-A744 TCGA-SJ-A6ZI TCGA-SJ-A6ZJ TCGA-SL-A6J9 TCGA-SL-A6JA 
       14.83        14.07        18.28         0.07         0.23 

  DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE 
                         0.30                          0.07 
  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 
                        20.05                         23.47 
[1] "0.3 - 113.4 (20.1)" "0.1 - 191.8 (23.5)"
[1] "hr=" "2.8"
D100V2, continuous
                               vv
clus                            ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA
  DEL PEAK 49(XP21.1) MUTATED                                        31
  DEL PEAK 49(XP21.1) WILD-TYPE                                     364
                               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                                  50
  DEL PEAK 49(XP21.1) WILD-TYPE                                62
D100V3, multiclass
                                         clus
vv                                        DEL PEAK 49(XP21.1) MUTATED
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                          31
  MIXED SEROUS AND ENDOMETRIOID                                     3
  SEROUS ENDOMETRIAL ADENOCARCINOMA                                50
                                         clus
vv                                        DEL PEAK 49(XP21.1) WILD-TYPE
  ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA                           364
  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"
D100V4, binary
                               cls
clus                              0   1
  DEL PEAK 49(XP21.1) MUTATED    17  67
  DEL PEAK 49(XP21.1) WILD-TYPE 124 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED     17   67
  DEL PEAK 49(XP21.1) WILD-TYPE  124  320
     clus
vv    DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  NO                           17                           124
  YES                          67                           320
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 49(XP21.1) MUTATED    53   2   6   6
  DEL PEAK 49(XP21.1) WILD-TYPE 310  21  11  29
D100V5, multiclass
    clus
vv   DEL PEAK 49(XP21.1) MUTATED DEL PEAK 49(XP21.1) WILD-TYPE
  R0                          53                           310
  R1                           2                            21
  R2                           6                            11
  RX                           6                            29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 49(XP21.1) MUTATED                                  1     1
  DEL PEAK 49(XP21.1) WILD-TYPE                                3    19
                               vv
clus                            BLACK OR AFRICAN AMERICAN
  DEL PEAK 49(XP21.1) MUTATED                          28
  DEL PEAK 49(XP21.1) WILD-TYPE                        73
                               vv
clus                            NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  DEL PEAK 49(XP21.1) MUTATED                                           1    47
  DEL PEAK 49(XP21.1) WILD-TYPE                                         8   319
D100V6, multiclass
                                           clus
vv                                          DEL PEAK 49(XP21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                                    1
  ASIAN                                                               1
  BLACK OR AFRICAN AMERICAN                                          28
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                           1
  WHITE                                                              47
                                           clus
vv                                          DEL PEAK 49(XP21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                                      3
  ASIAN                                                                19
  BLACK OR AFRICAN AMERICAN                                            73
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER                             8
  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"
D100V7, binary
                               cls
clus                              0   1
  DEL PEAK 49(XP21.1) MUTATED     4  57
  DEL PEAK 49(XP21.1) WILD-TYPE  10 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 49(XP21.1) MUTATED      4   57
  DEL PEAK 49(XP21.1) WILD-TYPE   10  310
                        clus
vv                       DEL PEAK 49(XP21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       DEL PEAK 49(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                10
  NOT HISPANIC OR LATINO                           310
[1] 2 2
[1] FALSE
